title: SRSF9 eCLIP replicate 1

city: La Jolla

first: Gene

middle: W

last: Yeo

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

institute: University of California, San Diego

description: Immunoprecipitate

data_processing:
Takes output from raw files. Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2. Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads. Command: STAR --runMode alignReads --runThreadN 16 --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All --readFilesCommand zcat --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep. Maps unique reads to the human genome. Command: STAR --runMode alignReads --runThreadN 16 --genomeDir /path/to/STAR_database_file --genomeLoad LoadAndRemove --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1 /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2 --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
Takes output from STAR genome mapping. Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE. Sorts resulting bam file for use downstream. Command: java -Xmx2048m -XX:+UseParallelOldGC -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Djava.io.tmpdir=/full/path/to/files/.queue/tmp -cp /path/to/gatk/dist/Queue.jar net.sf.picard.sam.SortSam INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam TMP_DIR=/full/path/to/files/.queue/tmp OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam VALIDATION_STRINGENCY=SILENT SO=coordinate CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream. Command: samtools index /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files. Merges the two technical replicates for further downstream analysis. Command: samtools merge /full/path/to/files/CombinedID.merged.bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream. Command: samtools index /full/path/to/files/CombinedID.merged.bam /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam. Only outputs the second read in each pair for use with single stranded peak caller. This is the final bam file to perform analysis on. Command: samtools view -hb -f 128 /full/path/to/files/CombinedID.merged.bam > /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view. Calls peaks on those files. Command: clipper -b /full/path/to/files/CombinedID.merged.r2.bam -s hg19 -o /full/path/to/files/CombinedID.merged.r2.peaks.bed --bonferroni --superlocal --threshold-method binomial --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format. Maps the raw reads to both hg19 and mm10 respectively. Describes the mapped reads from the eCLIP experiments.
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding (on hg19 and mm10 respectively); column 4 contains -log10(p-value) and column 5 contains log2(fold-enrichment) in eCLIP versus paired size-matched input

growth_protocol: Steady-state growth

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.  After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.
Protocol as described in Van Nostrand et al, Nature Methods (2016) https://www.ncbi.nlm.nih.gov/pubmed/27018577
eCLIP-seq

treatment_protocol: HEK 293 cells cultured to 50% confluency in 10 cm plates in DMEM with 10%  (v/v) FBS   were co-transfected with 0.4 g of minigene gIQEQ, 1.0 mg of TAG and 4mg of HA-tagged SRSF9 (HA-SRSF9) using lipofectamine 2000 (Invitrogen). While plated, cells were crosslinked with UV (254 nm, 400 mJ/cm2). Cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen.

tag: tag

value: HA

tag: sample type

tag: antibody company

value: Sigma


title: SRSF9 eCLIP replicate 2

status: Public on Apr 17 2018

type: SRA

country: USA

description: Immunoprecipitate

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: BR145

city: San Diego

first: YING

last: DING

state: CA

address: 10777 Science Center Dr.

department: Computational Biology

institute: Pfizer

description:
expression_tpm.txt
The raw data were submitted to EGA
EGA study accession: EGAS00001002621
https://www.ebi.ac.uk/ega/studies/EGAS00001002621

data_processing:
Gene expression (TPM) was predicted from RNA-Seq data of 178 SMC samples (168 tumors, 10 normals) using RSEM, hg19 as the genome reference and the same gene model library as used by Omicsoft
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited data matrix include TPM values with samples as columns and genes as rows

source_name: Primary Tumor

extract_protocol: sequencing libraries were prepared using TruSeq RNA Sample Preparation kit v2 (RS-122-2001 and RS-122-2002, Illumina).

tag: cell type

value: Primary Tumor

value: late

tag: ihc

value: TN

value: pre


title: Hek 293T : NIH/3T3

city: Cambridge

first: Christopher

last: Fincher

state: MA

address: 455 Main St

institute: Whitehead Institute

description:
processed data file:
SpeciesMixing_human.dge.txt.gz
SpeciesMixing_mouse.dge.txt.gz

data_processing:
Basecalls were performed using bcl2fastq. A single bam file was generated from paired-end fastq files for each Drop-seq run using the Picard Tool FastqToSam.
Sample 20 was downsampled to ~300M reads prior to data processing.The ‘Drop-seq core computational protocol’, v1.2, as developed by Jim Nemesh in the McCaroll lab (http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf), was used to process and align the sequencing data. Briefly, sequencing reads were tagged with their associated cell and molecular barcodes, followed by the trimming of 5’ primer and 3’ polyA sequences. Sequences generated from asexual animals were mapped using bowtie to the dd_Smed_v4 transcriptome assembly with the following parameters [--best –S]. The following sequences were added to the transcriptome assembly for mapping: dd_Smed_v4_0_0_1, dd_Smed_v4_7_0_1, dd_Smed_v4_4_1_1, mtRNA_1, mtRNA_2, and SMED_11901_V2. Sequences generated from sexual animals were mapped using bowtie to the uc_smed_v2 reference transcriptome with the following parameters [--best –S]. Sequences generated from cultured cells were mapped using STAR to a mixed human + mouse genome (http://mccarrolllab.com/dropseq/).
Using the DetectBeadSynthesisErrors module [NUM_BARCODES=2X expected cell number, PRIMER_SEQUENCE=AAGCAGTGGTATCAACGCAGAGTAC], errors in barcode sequence associated with bead synthesis were detected and were either corrected, if possible, or the associated reads were removed. The number of cells in a run was estimated by plotting the cumulative distribution of number of reads per cell. The number of cells at the inflection point was used as the estimated cell number in the data. A gene expression matrix was generated for the expected number of cells using the module DigitalExpression [NUM_CORE_BARCODES= # cells at inflection point] (http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf). Contig isoforms for sequences generated from asexual animals were then merged by summing the mapped reads to each isoform. Finally, cell IDs were tagged with their body section of origin, and the resulting expression matrices were combined.
Generation of the mixed species plot for cultured cell data was performed as described in the ‘Drop-seq core computational protocol’ (http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf).
For the principal sequencing, cells with more than 18,000 unique molecular identifiers (UMIs) and cells expressing less than 500 genes were removed from the data to ensure that low quality cells and potential cell doublets were not present. Five transcripts identified as ribosomal or mitochondrial by BLAST (dd_Smed_v4_0_0_1, dd_Smed_v4_7_0_1, dd_Smed_v4_4_1_1, mtRNA_1, and mtRNA_2) were removed. For the targeted sequencing of brain cells, cells with more than 15,400 unique molecular identifiers (UMIs) and cells expressing less than 500 genes were removed from the data. Five transcripts identified as ribosomal or mitochondrial by BLAST (dd_Smed_v4_0_0_1, dd_Smed_v4_7_0_1, dd_Smed_v4_4_1_1, mtRNA_1, and mtRNA_2) were removed. For the sequencing from sexual animals, cells with more than 12,000 unique molecular identifiers (UMIs) and cells expressing less than 500 genes were removed from the data.
Genome_build:
Asexual Schmidtea mediterranea strain CIW4, reference transcriptome (dd_Smed_v4):
http://planmine.mpi-cbg.de/planmine/aspect.do?name=Transcriptomes
sexual Schmidtea mediterranea strain S2F1L3F2L3, reference transcriptome (uc_Smed_v2):
http://hdl.handle.net/2142/28689
mixed mouse and human cell lines, reference genome (hg19_mm10):
http://mccarrolllab.com/dropseq/

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: 1:1 mixture of Hek293T : NIH/3T3 cultured cells

growth_protocol: All cultured cell lines were cultured at 37°C with 5% CO2 in DMEM (Invitrogen) supplemented with 10% FBS (Life Technologies) and 1% penicillin-streptomycin (Thermo Fisher Scientific). Asexual Schmidtea mediterranea strain (CIW4) and sexual strain (S2F1L3F2L3) animals were starved 7 days prior to dissection.

extract_protocol:
Planarian body sections were cut into small fragments (<1mm) and transferred to a 50 mL tube with CMFB (400mg/L NaH2PO4, 800mg/L NaCl, 1200 mg/L KCl, 800 mg/L NaHCO3, 240 mg/L glucose, 1% BSA, 15mM HEPES, pH7.3). Volume was brought to 45 mL with CMFB, to which 5 mL collagenase (1 mg/ml; Sigma-aldrich, C0130) was added. Suspension was generated through agitation of the mixture for 5-10 minutes using pipettes. Cell suspension was passed through a 40μm filter and centrifuged at 1250 rpm for 5 minutes. The supernatant was removed and cells were resuspended in 1 mL of CMFB. Single cell suspensions were stained with Hoechst 33342 (40 μl/ml, Invitrogen) and propidium iodide (3 μl/ml, Sigma-aldrich). Living cells were sorted by flow cytometry into 5 mL tubes. In seven samples, cells with 4C DNA content as determined by high Hoechst signal were gated out. Following FACS, cells were isolated in droplets with barcoded beads using Drop-seq (http://mccarrolllab.com/download/905/). Briefly, cells were lysed within droplets, capturing polyA RNA onto barcoded beads. Barcoded beads were isolated and used to generate cDNA. Beads with attached cDNA were exonuclease treated and cDNA was amplified by PCR. Pairs of PCR reactions were purified using 0.6X AMPure XP beads (Agencourt).  Prior to Drop-seq runs, cultured cells were grown to confluence. Cells were washed once with 1X PBS. NIH/3T3 cells were then treated with TrypLE (Invitrogen) for five minutes and quenched and resuspended in an equal volume of growth medium. 293 T cells were resuspended in 1X PBS by manual dissociation. Cells were spun down at 300xg for five minutes and resuspended in 1X PBS + 0.01% BSA. Cells were spun down again at 300xg for three minutes and resuspended in 1 mL 1X PBS. Cells were passed through a 40μm filter and counted. 1X PBS + 0.01% BSA was used to generate input for Drop-seq runs (http://mccarrolllab.com/download/905/).
A single library was generated for each Drop-seq run using 600pg purified, amplified cDNA using Nextera XT (Illumina). Libraries were purified by two rounds of AMPure XP purification (0.6X, 1X) (http://mccarrolllab.com/download/905/).

tag: strain/cell line

value: Hek293T, NIH/3T3

tag: tissue

value: 1:1 mixture of Hek293T:NIH/3T3 cultured cells

tag: facs gate

tag: drop-seq run number (per biological sample)


title: IgG

description: Immunoprecipitate

value: IgG

value: Sino Biotchnology


title: BR018


title: Input replicate 2

description: Whole-cell lysate

value: input


title: BR200


title: A549res-34µM_1

type: RNA

city: Bonn

first: Ganna

last: Kalayda

address: An der Immenburg 4

department: Clinical Pharmacy

country: Germany

institute: University of Bonn

description: gene expression in res. cells after treatment with 34µM

hyb_protocol: After purifying the labelled/amplified complementary RNA (cRNA) using silica-membrane RNeasy spin columns from the RNeasy® Mini Kit (Qiagen, Venlo, the Netherlands), cRNA was quantified spectrophotometrically using NanoDropTM ND-1000 (Thermo Fisher Scientific Inc., Waltham, MA, USA). 40 µL of equivalent amounts of Cy3-labelled cRNA in 10x Blocking Agent and 25x Fragmentation Buffer, diluted with 2x GEx HI-RPM Hybridization Buffer were loaded on the gaskets of the microarray slide and kept at 65 °C for 17 h with 10 rpm of agitation.

scan_protocol: After washing twice with different washing buffers, the microarray was read out with the SureScan Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA) to obtain immunofluorescence intensity.

data_processing: Array data were pre-processed via background correction (exponential convolution method) and quantile normalization. Statistical significances of dose- and resistance-induced gene expression changes were analysed using limma, a linear model-based technique. Differential expression was declared at a 5 % false discovery rate (FDR) cut-off together with an at least twofold up- or downregulation. The overall significance of the signature of differentially expressed genes was assessed via a global test. VALUE contains quantile normalized data for probes with REFSEQ IDs only (29,729)

source_name: NSCLC, cisplatin resistant, 24h cisplatin, 34uM

label_protocol: Transcriptome was then analysed using One-Color Whole Genome Array SurePrint G3 Human GE V2 8x60K Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions. Briefly, total RNA was transcribed to complementary deoxyribonucleic acid (cDNA) using AffinityScript-RT, Oligo dT-Promoter Primer and T7 RNA Polymerase and labelled using the One Colour RNA Spike-In Kit (positive controls) including Cyanin 3-CTP (Cy3) dye.

growth_protocol: The human NSCLC cell line A549 was obtained from American Type Culture Collection (ATCC) (Manassas, VA, USA). Its cisplatin-resistant sub-line A549rCDDP2000 derived from the Resistant Cancer Cell Line (RCCL) collection (www.kent.ac.uk/stms/cmp/RCCL/RCCLabout.html) had been established by adapting the growth of A549 cells in the presence of increasing concentrations of cisplatin until a final concentration of 2000 ng/mL cisplatin. A549 cells were grown in IMDM medium (PAN-Biotech, Aidenbach, Germany) containing 4 mM L-glutamine supplemented with 10 % foetal calf serum, 100 I.E./mL penicillin and 0.1 mg/mL streptomycin. The medium of the A549rCDDP2000 cells additionally contained 2 µg/mL cisplatin. Cells were cultivated as monolayers in a humidified atmosphere at 37 °C and 5 % CO2.

extract_protocol: Total ribonucleic acid (RNA) was isolated from the cells with my-Budget RNA Mini Kit (Bio-Budget, Krefeld, Germany) through different spin columns according to the manufacturer’s instructions. Isolated RNA was stored at -80 °C until analysis was performed.

treatment_protocol: For all experiments, cells were allowed to attach overnight, experienced 4 h of serum starvation and were subsequently treated with cisplatin for 24 h in IMDM medium without any supplements. The parental cells were treated with 11 µM cisplatin. The resistant sub-line was exposed to 11 µM cisplatin and additionally treated with 34 µM cisplatin. The control cells were treated with the drug-free medium.

tag: sensitivity

value: resistant

tag: treatment conc


title: A549res-ctrl_1

description: gene expression in untreated res. cells

source_name: NSCLC, cisplatin resistant, control


title: A549res-11µM_1

description: gene expression in res. cells after treatment with 11µM

source_name: NSCLC, cisplatin resistant, 24h cisplatin, 11uM


title: BR196

value: early

value: ER+


title: A549sens-ctrl_1

description: gene expression in untreated sens. cells

source_name: NSCLC, cisplatin sensitive, control

value: sensitive


title: Pooled_input

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

library_source: genomic

data_processing:
ChIP-seq reads from samples 1 and 2 were mapped to the human reference genome (GRCh37/hg19) using the bwa-0.6.1 with default parameters. Aligned and unaligned reads and their quality strings are contained in resulting bam files. Therefore, bam files are provided as raw data
ChIP seq reads from samples 3 and 4 were mapped to the human reference genome (GRCh37/hg19) using the bwa-0.7.12 with default parameters. Aligned and unaligned reads and their quality strings are contained in resulting bam files. Therefore, bam files are provided as raw data
Peak locations for BRD4 and H3K27 ChIP experiments were determined using the MACS -1.4.2 with a cutoff p-value of 1E-7 for narrow peaks and 1E-1 for broad peaks
Enriched regions for Pol2 ChIP experiments were identified using the SICER algorithm with a cutoff FDR of 1E-10 and gap parameter of 600bp
ChIP peak regions from multiple samples (of the same ChIP type) were merged, and aligned reads for these newly defined regions were caluclated (even for those where no peak was called). Then the resulting regions were annotated with gene information by calculating distances from RefSeq gene starts and ends to the center of the newly defined peak regions.
ATAC-seq reads were mapped to the human reference genome (GRCh37/hg19) using the Bowtie2-2.2.6 with maximum fragment length of 1000 and no-mixed mode. Duplicates marked with Picard-1.140.
DNase2hotspots software package (https://sourceforge.net/projects/dnase2hotspots) was used to identify hotspots (enriched regions) from ATAC-seq
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Combined peak regions and scores of ChIP data are in Microsoft Excel files
Supplementary_files_format_and_content: ATAC-seq hotspots are reported in form of bedgraphs

molecule: genomic DNA

source_name: B-Chronic Lymphocytic Leukemia (CLL) cels

growth_protocol: RPMI 10% FBS

extract_protocol:
extract_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: a=baseline; b=4 hours stimulation with 3.2uM of CpG oligonucleotide; c=4 hours stimulation with 3.2uM of CpG oligonucleotide + 1 uM of BET inhibitor (PLX51107)

value: Primary B-CLL cells


title: Input replicate 1

description: Whole-cell lysate


title: BR183


title: A549sens-11µM_1

description: gene expression in sens. cells after treatment with 11µM

source_name: NSCLC, cisplatin sensitive, 24h cisplatin, 11uM


title: LD_ZT14_B (XR-seq)

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

data_processing:
Library strategy: XR-seq
adapter trimming with cutadapt ath 3' end. The adapter is TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG
genome alignment onto TAIR10 by using Bowtie with the following parameters: : --nomaqround --phred33-quals -e 70
read deduplication
read count for each gene for both strands distinctly using bedtools
RPKM normalization
Genome_build: TAIR10
Supplementary_files_format_and_content: tab separated gene tables (txt) of the normalized TS (transcribed strand) and NTS (non-transcribed strand) repair (RPKM).

organism: Arabidopsis thaliana

source_name: LD_ZT14, whole plant

growth_protocol: 10-days-old seedlings of Arabidopsis thaliana ecotype Columbia (Col-0) were used. Plants were grown under a long-day condition (16 h light /8 h dark) with a cool white fluorescent light at 24°C. 8 mg of seeds for each sample were surface-sterilized, and stratified for 2 days at 4°C, and then planted on a Murashige and Skoog (MS) plate. For circadian clock experiments, seedlings were collected in 3-h intervals (ZT1, ZT4, ZT7, ZT10, ZT13, ZT16, ZT19, and ZT22).

extract_protocol:
After 30-min incubation in the dark at 24°C, the seedlings were frozen with liquid nitrogen, and were ground using mortar and pestle. The resulting powder was resuspended in 400 µl of STES buffer (200 mM Tris⋅HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 10 mM EDTA) and 400 µl of phenol:chloroform (20:1). The sample was homogenized by vortexing with acid-washed glass beads for 30 min at 4°C, followed by centrifugation at 14000 rpm for 10 min at room temperature. The supernatant was treated with 10 µl of RNAseA (R4642; Sigma) for 1 hour at 37°C, then with 10 µl of proteinase K (P8107S; NEB) for 1 hour at 60°C. The excision products were precipitated by ethanol precipitation, and purified by immunoprecipitation with a CPD-specific antibody. These fragments were 3′ end radiolabeled with [α- 32P]-3′-deoxyadenosine 5′-triphosphate (cordycepin 5′-triphosphate) (Perkin-Elmer) by terminal deoxynucleotidyl transferase (NEB), and visualized on an 11% sequencing gel.
Excision products were purified as above. 5’ and 3’ adapters compatible with the Illumina TruSeq Small RNA protocol were ligated to excision products. Ligation products were immunoprecipitated with CPD antibodies, then photoreversed with photolyase. Analytical PCR was performed using one percent of the sample to decide the minimum number of cycles required for preparative scale PCR amplification (fig S2B). The repaired ligation products were PCR-amplified using 50- and 63-nt-long primers adding specific barcodes compatible with the Illumina TruSeq Small RNA kit. The correct size PCR products representing the library were gel purified, and then sequenced in the Illumina HiSeq 4000 (experiment 1) and 2500 (experiment 2) platforms, and single-end 50-nt reads were generated.

treatment_protocol: 10-days old seedlings were irradiated with 120 J/m2 UVC (254 nm).

tag: ecotype

tag: experiment

tag: time

value: seedlings


title: BR195


title: BR194


title: Pol2_ChIPseq_4c

description:
0086Ohio_Pol2_actregs.xlsx
18_01VI_0086Ohio_4c-PLX5stimul_Pol2_hg19_i74

tag: protocol

value: 4 hours stimulation with 3.2uM of CpG oligonucleotide + 1 uM of BET inhibitor (PLX51107)

tag: chip-antibody

value: anti-RNA Pol II (Active Motif #39097)


title: BR188

value: Primary Tumor


title: Pol2_ChIPseq_4b

description:
0086Ohio_Pol2_actregs.xlsx
17_01VH_0086Ohio_4b-stimulated_Pol2_hg19_i73

value: 4 hours stimulation with 3.2uM of CpG oligonucleotide


title: Pol2_ChIPseq_3c

description:
0086Ohio_Pol2_actregs.xlsx
15_01UU_0086Ohio_3c-PLX5stimul_Pol2_hg19_i71


title: BR187

value: late


title: PANC-1, control (miRNA)

city: Nanning

first: Qiao

last: Yu

address: Shuangyong road, qingxiu district，nanning

country: China

institute: First Affiliated Hospital of Guangxi Medical University

description: O

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Feature Extraction (FE) is the process by which information from probe features is extracted from microarray scan data.

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R

source_name: PANC-1, rapamycin

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: The human pancreatic cancer cell line PANC-1 was cultured in complete Dulbecco’s modified Eagle’s medium (DMEM).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The PANC-1 cells treated with 100 µM rapamycin were preferred as the autophagy-induced group(group B), and cells cultured by DMEM were selected as the control group(group O)

tag: cell line

value: pancreatic cancer cell

tag: agent

value: control


title: Tamoxifen treated #2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Tamoxifen-exposed mice 4 weeks after tamoxifen withdrawal and treated with E2 for 8h.

hyb_protocol: The array was prehybridized, washed, and stained with streptavidin-phycoerythrin in the automated Affymetrix Gene Chip Fluidics Station 400.

scan_protocol: Fluorescent intensities were captured using an Affymetrix GeneChip confocal Scanner (Agilent Technologies) and the raw image (.DAT) and intensity (.CEL) files were generated using Affymetrix MAS5.0 software.

data_processing:
Chip quality was assessed using various parameters outputted by the following combination of software packages: MAS5.0, BRB Array tools and Bioconductor Version 1.2. Normalization and model-based expression values were determined using the Robust Multichip Analysis method.
Genome build: mm9
Set of exons used: Comprehensive/Extended

label: Biotin

organism: Mus musculus

source_name: Mammary epithelial cells, p53-null, tamoxifen treated

label_protocol: According to Affymetrix protocol.

growth_protocol: All donor and recipient mice were bred and maintained at Baylor College of Medicine. The donor mice were Balb/c p53-null mammary gland, and the recipient mice were Balb/c p53 WT. All mice were maintained in a conventional mouse facility with room temperature set at 22°C, with food and water provided ad libitum. The animal facility is accredited by the American Association of Laboratory Animal Care and all the animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) at Baylor College of Medicine. Mammary epithelial cells (MECs) were isolated following a protocol previously published. Briefly, #4 mammary gland transplants were collected and intramammary lymph nodes were removed. Each group of mammary glands were pooled, finely minced and transferred into a sterile 50 mL tube containing 10 mL of DMEM/F12 media with antibiotics supplemented with collagenase (2 mg/ml) and hyaluronidase 100U/ml mixture. The tubes were kept at a 45o angle in a 37oC shaker for 3h. The dispersion was further facilitated by mechanically shaking vigorously a few times. The mammary epithelial cells released by this digestion were centrifuged at 1000X g for 5 min and washed 4 times in PBS with 5% serum to eliminate fat cells and the remaining collagenase. Cells were re-suspended with serum-free PBS. Cell viability was assessed by trypan blue exclusion.

extract_protocol: For microarray and quantitative Real-Time PCR (qPCR), total mammary epithelial cell RNA or total mammary gland RNA was isolated from #4 glands (lymph nodes removed) using the RNeasy Lipid Tissue Midi Kit according to the manufacturer's instructions (QIAGEN, Inc., Valencia, CA). Physical integrity of the RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA); RNA quantitation was performed using the NanoDrop ND1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). For microarray and qPCR analysis, total RNA pooled from a set of three to five mice per treatment group was analyzed.

treatment_protocol: The basic transplantation protocol was previously described. Briefly, the inguinal (#4) mammary fat pads of three-week-old Balb/c WT mice were cleared. Five weeks after fat pad clearance, 1-mm2 fragments of mammary duct from 8-week-old female p53-null mice were transplanted into both cleared inguinal mammary fat pads. The transplanted cells take 8 weeks to completely fill the fat pad, at which point the cells assume a steady-state level of proliferation. Thus, tamoxifen treatment was started at 8-week-old hosts' age to avoid any effects of the agents on the ability of the cells to grow and fill the fat pad. At 8 weeks of host age, mice received a 5 mg tamoxifen (TAM) pellet or sham (control) pellet subcutaneously (SC) on the back. The pellets remained in place for 13 weeks before removal. At 4 weeks or 8 weeks after cessation of tamoxifen, all mice were injected with 17β-Estradiol (100μg SC). After 8h of 17β-Estradiol (E2) treatment, all mice were sacrificed and #4 mammary gland transplants were collected. Mammary epithelial cells were isolated by collagenase digestion.

value: mammary epithelial cells (MECs)

tag: strain/background

value: Balb/c

tag: genotype/variation

tag: treatment 1

value: tamoxifen

tag: treatment 2

value: 17-beta-estradiol (E2) for 8h


title: Pol2_ChIPseq_3b

description:
0086Ohio_Pol2_actregs.xlsx
14_01UT_0086Ohio_3b-stimulated_Pol2_hg19_i70

tag: cell type


title: BR181

tag: ihc

value: pre


title: Tamoxifen treated #3


title: Pol2_ChIPseq_3a

description:
0086Ohio_Pol2_actregs.xlsx
13_01US_0086Ohio_3a-vehicle_Pol2_hg19_i69

value: baseline


title: Control #3

description: Control mice treated with E2 for 8h.

source_name: Mammary epithelial cells, p53-null, control


title: PANC-1, rapamycin (miRNA)

description: B

value: rapamycin


title: Tamoxifen treated #1


title: Pol2_ChIPseq_2c

description:
0007Ohio_CLL_Pol2_2nd_actregs.xlsx
18_0007Ohio_CLL_Patient_2c_Pol2_hs_i6


title: BR182


title: BR176

value: early

value: TN


title: Pol2_ChIPseq_2b

description:
0007Ohio_CLL_Pol2_2nd_actregs.xlsx
17_0007Ohio_CLL_Patient_2b_Pol2_hs_i3

value: Primary B-CLL cells


title: BR175

value: ER+


title: Pol2_ChIPseq_2a

description:
0007Ohio_CLL_Pol2_2nd_actregs.xlsx
16_0007Ohio_CLL_Patient_2a_Pol2_hs_i90

value: anti-RNA Pol II (Active Motif #39097)


title: BR170

value: Primary Tumor


title: Pol2_ChIPseq_4a

description:
0086Ohio_Pol2_actregs.xlsx
16_01VG_0086Ohio_4a-vehicle_Pol2_hg19_i72


title: BR167


title: Pol2_ChIPseq_1c

description:
0007Ohio_CLL_Pol2_2nd_actregs.xlsx
15_0007Ohio_CLL_Patient_1c_Pol2_hs_i87

value: 4 hours stimulation with 3.2uM of CpG oligonucleotide + 1 uM of BET inhibitor (PLX51107)


title: Pol2_ChIPseq_1b

description:
0007Ohio_CLL_Pol2_2nd_actregs.xlsx
14_0007Ohio_CLL_Patient_1b_Pol2_hs_i84

value: 4 hours stimulation with 3.2uM of CpG oligonucleotide


title: Control #1

description: Control mice treated with E2 for 8h.


title: BR164

description:
expression_tpm.txt
The raw data were submitted to EGA
EGA study accession: EGAS00001002621
https://www.ebi.ac.uk/ega/studies/EGAS00001002621


title: Pol2_ChIPseq_1a

description:
0007Ohio_CLL_Pol2_2nd_actregs.xlsx
13_0007Ohio_CLL_Patient_1a_Pol2_hs_i81


title: BR161


title: BR159

value: late


title: BR154


title: Control #2

description: Control mice treated with E2 for 8h.

value: control


title: H3K27Ac_ChIPseq_4c

description:
0086Ohio_CLL_H3K27Ac_actregs.xlsx
12_01UR_0086Ohio_4c-PLX5stimul_H3K27Ac_hg19_i68

value: H3K27ac (Active Motif #39133)


title: Individual 7

city: Irvine

first: Kai

last: Kessenbrock

address: 839 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

data_processing:
Alignment of 3’ end counting libraries from droplet-enabled scRNAseq analyses was completed utilizing 10x Genomics Cell Ranger 1.3.1
Each library was aligned to an indexed GRCh38 genome using Cell Ranger Count. “Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cells across the libraries from different individuals.
Genome_build: GrCH38
Supplementary_files_format_and_content: Processed Data files are tab-delimited .txt files of counts expression matrices corresponding to each of the libraries generated from the 4 individuals in this study

source_name: Mammoplasty Reduction

extract_protocol:
Viable organoids were thawed and washed using DMEM, and digested with 0.05% trypsin (Corning 25-052-CI) containing DNase (Sigma Aldrich D4263-5VL) to generate single cell suspension. Cells were stained for FACS using fluorescently labeled antibodies for CD31 (eBiosciences 48-0319-42), CD45 (eBiosciences 48-9459-42), EpCAM (eBiosciences 50-9326-42), CD49f (eBiosciences 12-0495-82), SytoxBlue (Life Technologies S34857). We only proceeded with samples showing at least 80% viability as measured using SytoxBlue in FACS
flow cytometry sorted cells were washed in PBS with 0.04% BSA and reseupended at a concentration of approximately 1000 cells/µl. Library generation for 10x Genomics v1 chemistry was performed following the Chromium Single Cell 3’ Reagents Kits User Guide: CG00026 Rev B. Library generation for 10x Genomics v2 chemistry were performed following the Chromium Single Cell 3’ Reagents Kits v2 User Guide: CG00052 Rev B.

treatment_protocol: Samples were washed in PBS (Corning 21-031-CV) and mechanically dissociated using a razor blade. Dissociated samples were digested overnight in DMEM (Corning 10-013-CV) with Collagenase Type I, 2 mg/mL (Life Technologies 17100-017). Viable organoids were separated using differential centrifugation and viably frozen in 50% FBS (Omega Scientific FB-12), 40% DMEM, and 10% DMSO (Sigma-Aldrich D8418) by volume.

tag: Sex

value: female

tag: tissue

value: Adult Human Breast Epithelium


title: Individual 6


title: H3K27Ac_ChIPseq_4a

description:
0086Ohio_CLL_H3K27Ac_actregs.xlsx
10_01UP_0086Ohio_4a-vehicle_H3K27Ac_hg19_i89


title: H3K27Ac_ChIPseq_4b

description:
0086Ohio_CLL_H3K27Ac_actregs.xlsx
11_01UQ_0086Ohio_4b-stimulated_H3K27Ac_hg19_i90


title: H3K27Ac_ChIPseq_3c

description:
0086Ohio_CLL_H3K27Ac_actregs.xlsx
09_01UO_0086Ohio_3c-PLX5stimul_H3K27Ac_hg19_i88


title: BR148


title: BR152


title: BR100


title: H3K27Ac_ChIPseq_3b

description:
0086Ohio_CLL_H3K27Ac_actregs.xlsx
08_01UN_0086Ohio_3b-stimulated_H3K27Ac_hg19_i87


title: Individual 5


title: H3K27Ac_ChIPseq_2c

description:
0007Ohio_CLL_H3K27Ac_2nd_actregs.xlsx
12_0007Ohio_CLL_Patient_2c_H3K27Ac_hs_i5


title: H3K27Ac_ChIPseq_3a

description:
0086Ohio_CLL_H3K27Ac_actregs.xlsx
07_01UM_0086Ohio_3a-vehicle_H3K27Ac_hg19_i86


title: BR136


title: ATACseq_4c


title: HWA_pCHiC

city: Princeton

first: Kristina

middle: Marie

last: Garske

email: kmgarske@ucla.edu, kg8086@princeton.edu

state: New Jersey

address: Carl Icahn Lab, South Drive, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics; Ecology & Evolutionary Biology

institute: Princeton University

data_processing:
Reduce number of sequencing reads to ~135M reads to match the number used in (Mifsud et al., Nature Genetics, 2015) analysis of their CHi-C data.
Sequencing reads were processed with the Hi-C User Pipeline (HiCUP) software v 0.5.8, aligning reads to the human reference genome (GRCh37/hg19) and using all HiCUP default parameters.
Significant chromosomal interactions were called with the Capture Hi-C Analysis of Genome Organization (CHiCAGO) software v 1.2.0, using default parameters, including the threshold of 5 for calling significant interactions.
Genome_build: hg19
Supplementary_files_format_and_content: Text file lists the baited (promoter-containing) HindIII fragment and the interacting (other end) HindIII fragment as well as the interaction score from the CHiCAGO software

source_name: Human white adipocytes

growth_protocol: Primary human white preadipocyte (HWP) cells were obtained and cultured as recommended by PromoCell (PromoCell C-12731, lot 395Z024) for preadipocyte growth and differentiation into adipocytes. Cell media (PromoCell) was supplemented with 1% penicillin-streptomycin. We maintained the cells at 37ºC in a humidified atmosphere at 5% CO2.

extract_protocol:
10M adherent HWA were rinsed with serum-free media prior to fixation. We fixed the HWA directly in culture plates with 2% formaldehyde (EMD Millipore 344198) in serum-free adipocyte nutrition media (PromoCell). We incubated cells in fixation medium with rocking at room temperature for 10 minutes, and then quenched with 1 M ice-cold glycine for a final concentration of 125 mM. After 5 minutes of rocking incubation at room temperature, we rinsed fixed cells twice with ice-cold PBS. Then we incubated the cells with rocking on ice with ice-cold permeabilization buffer (10 mM Tris–HCl pH 8, 10 mM NaCl, 0.2 % Igepal CA-630, Complete EDTA-free protease inhibitor cocktail [Roche])36 for 30 minutes. We scraped cells from the culture plate and centrifuged at 2500 x g for 5 minutes at 4ᵒC to pellet nuclei. The supernatant was discarded and nuclei were flash frozen in liquid nitrogen and put at -80ºC.
The Hi-C library was prepared as described in (Rao et al., Cell, 2014) with modifications. We processed 10M HWA nuclei in 5M cell aliquots, closely following Rao et al. protocol I.a.1 except we digested chromatin with 400U of HindIII (New England Biolabs R3104) at 37ºC overnight with shaking (950 rpm). After digestion, we pelleted nuclei with centrifugation at 2500 x g for 5 minutes at 4ºC. We performed end-filling and marked with biotin using biotin-14-dCTP (Invitrogen 19518-018), performed in-nucleus ligation, degraded protein using Proteinase K, and performed ethanol precipitation and purification. We sheared 5 μg of DNA to 250-550 bp using the Covaris M220 instrument. We performed double size-selection to retain fragments from 250-550 bp using Agencourt AMPure XP beads (Beckman Coulter A63881). We immobilized the fragments containing biotin using DYNAL™ MyOne™ Dynabeads™ Streptavidin T1 (Invitrogen 65601) beads. After end-repair and attachment of dATP, we ligated Illumina paired-end adaptors to the bead-bound library following the SureSelectXT user manual for Illumina Paired-End Multiplexed Sequencing (Agilent Technologies). After washing, we resuspended the Hi-C library in 20 μl of 1x Tris buffer and subsequently removed the Streptavidin beads from the DNA by heating at 98ºC for 10 minutes. We then amplified the adaptor-ligated library using 8 PCR cycles and purified using Agencourt AMPure XP beads, following the SureSelectXT user manual. The RNA baits for promoter capture were designed in (Mifsud et al., Nature Genetics, 2015) for capturing HindIII fragments containing gene promoters (Dr. Cameron Osborne kindly shared the exact design). A total of 550 ng of the Hi-C library was hybridized to the biotinylated RNA baits, captured with DYNAL™ MyOne™ Dynabeads™ Streptavidin T1 beads, and amplified in a post-capture PCR to add indexes, using 12 PCR cycles. The library was sequenced on the Illumina HiSeq 4000 platform.

treatment_protocol: Primary human white adipocytes (HWA) were serum-starved for 16 hours using 0.5% fetal calf serum (FCS) in supplemented adipocyte basal medium (PromoCell), prior to treatment with 0.23% fatty acid free bovine serum albumin (BSA, Sigma Aldrich A8806) in media containing 0.5% FCS for 24 hours prior to fixation.

value: Primary human white preadipocytes differentiated into adipocytes in vitro

tag: passage


title: H3K27Ac_ChIPseq_2b

description:
0007Ohio_CLL_H3K27Ac_2nd_actregs.xlsx
11_0007Ohio_CLL_Patient_2b_H3K27Ac_hs_i92


title: Individual 4


title: BR143

value: pre


title: H3K27Ac_ChIPseq_2a

description:
0007Ohio_CLL_H3K27Ac_2nd_actregs.xlsx
10_0007Ohio_CLL_Patient_2a_H3K27Ac_hs_i89

value: baseline


title: BR128


title: ATACseq_4b


title: BR135


title: A549res-11µM_3

description: gene expression in res. cells after treatment with 11µM

tag: sensitivity

value: resistant

tag: treatment conc


title: BR127

value: early


title: H3K27Ac_ChIPseq_1c

description:
0007Ohio_CLL_H3K27Ac_2nd_actregs.xlsx
09_0007Ohio_CLL_Patient_1c_H3K27Ac_hs_i86


title: pV_M_ICF2_15

type: genomic

city: EVRY

first: Nizar

last: Touleimat

address: 2 rue Gaston Crémieux

department: Centre National de Génotypage

country: France

institute: Commissariat à l'Energie Atomique

description: ICF2 blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Control Software v3.2.45 using standard recommended Illumina scanner setting

data_processing:
GenomeStudio Software v2011.1 and pipeline described in Touleimat and Tost, Epigenomics 2012.
Unmethylated and methylated signal intensities in ICF_rawData.txt

label: Cy5 and Cy3

source_name: whole blood 22

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood using NucleoSpin®Tissue kit (Macherey-Nagel) according to manufacturer’s instructions

tag: gender

value: Male

value: Whole blood

tag: disease state


title: H3K27Ac_ChIPseq_1a

description:
0007Ohio_CLL_H3K27Ac_2nd_actregs.xlsx
07_0007Ohio_CLL_Patient_1a_H3K27Ac_hs_i80

value: Primary B-CLL cells

tag: protocol


title: A549sens-ctrl_2

description: gene expression in untreated sens. cells

value: sensitive


title: BR121

value: Primary Tumor

value: ER+


title: ATACseq_3b

value: 4 hours stimulation with 3.2uM of CpG oligonucleotide


title: P10_F_ICF2_14

description: ICF2 blood sample

source_name: whole blood 25

value: Female


title: CTL_F_26

description: normal blood sample

source_name: whole blood 24

value: normal


title: ATACseq_3c

value: 4 hours stimulation with 3.2uM of CpG oligonucleotide + 1 uM of BET inhibitor (PLX51107)


title: P3_F_ICF1_4

description: ICF1 blood sample

source_name: whole blood 23


title: ATACseq_4a


title: ATACseq_3a


title: BRD4_ChIPseq_4b

description:
0086Ohio_CLL_BRD4_actregs.xlsx
05_01UK_0086Ohio_4b-stimulated_BRD4_hg19_i83

tag: chip-antibody

value: BRD4 (Active Motif #A301-985A1)


title: BR124

source_name: Primary Tumor


title: P2_M_ICF1_5

description: ICF1 blood sample

source_name: whole blood 20


title: BRD4_ChIPseq_4a

description:
0086Ohio_CLL_BRD4_actregs.xlsx
04_01UJ_0086Ohio_4a-vehicle_BRD4_hg19_i82


title: BR112

description:
expression_tpm.txt
The raw data were submitted to EGA
EGA study accession: EGAS00001002621
https://www.ebi.ac.uk/ega/studies/EGAS00001002621

value: late


title: BRD4_ChIPseq_4c

description:
0086Ohio_CLL_BRD4_actregs.xlsx
06_01UL_0086Ohio_4c-PLX5stimul_BRD4_hg19_i84


title: ATACseq_2a


title: ATACseq_2c


title: pS_F_ICF3_12

description: ICF3 blood sample

source_name: whole blood 18


title: ATACseq_2b


title: H3K27Ac_ChIPseq_1b

description:
we ended up not using sample 08_0007Ohio_CLL_Patient_1b for analysis due to data quality issues
08_0007Ohio_CLL_Patient_1b_H3K27Ac_hs_i83

value: H3K27ac (Active Motif #39133)


title: BR108

value: TN

value: pre


title: ATACseq_1c


title: BR107


title: BR116


title: CTL_M_36

description: normal blood sample

source_name: whole blood 13


title: BR114


title: BR106


title: pD_M_ICF2_16

description: ICF2 blood sample

source_name: whole blood 17


title: BRD4_ChIPseq_3b

description:
0086Ohio_CLL_BRD4_actregs.xlsx
02_01UH_0086Ohio_3b-stimulated_BRD4_hg19_i80

source_name: B-Chronic Lymphocytic Leukemia (CLL) cels


title: ATACseq_1b


title: BRD4_ChIPseq_3c

description:
0086Ohio_CLL_BRD4_actregs.xlsx
03_01UI_0086Ohio_3c-PLX5stimul_BRD4_hg19_i81


title: ATACseq_1a

value: baseline


title: P6_M_ICF2_10

description: ICF2 blood sample

source_name: whole blood 16


title: Whole animal 1.2

description:
processed data file:
Saturation.txt.gz

organism: Schmidtea mediterranea

source_name: Whole animal

tag: strain/cell line

value: Whole animal

tag: facs gate

value: All Cells

tag: drop-seq run number (per biological sample)


title: CTL_F_11

description: normal blood sample

source_name: whole blood 11

value: Whole blood


title: CTL_F_15

description: normal blood sample

source_name: whole blood 12


title: pC_F_ICF3_5

description: ICF3 blood sample

source_name: whole blood 21


title: BR067


title: pG_M_ICF1_11

description: ICF1 blood sample

source_name: whole blood 7

value: Male


title: pU_M_ICF4_16

description: ICF4 blood sample

source_name: whole blood 10


title: CTL_M_24

description: normal blood sample

source_name: whole blood 19


title: CTL_F_42

description: normal blood sample

source_name: whole blood 15


title: BR103


title: pW_F_ICF1_1

description: ICF1 blood sample

source_name: whole blood 8


title: BRD4_ChIPseq_2b

description:
0007Ohio_CLL_BRD4_2nd_actregs.xlsx
05_0007Ohio_CLL_Patient_2b_BRD4_hs_i91

value: Primary B-CLL cells


title: BRD4_ChIPseq_2a

description:
0007Ohio_CLL_BRD4_2nd_actregs.xlsx
04_0007Ohio_CLL_Patient_2a_BRD4_hs_i88


title: Sexual 1.2

description:
processed data file:
SexualClusteringDigitalExpressionMatrix.dge.txt.gz

source_name: Square regions directly below sexual 1.1 regions


title: BRD4_ChIPseq_2c

description:
0007Ohio_CLL_BRD4_2nd_actregs.xlsx
06_0007Ohio_CLL_Patient_2c_BRD4_hs_i4


title: pR_F_ICF1_21

description: ICF1 blood sample

source_name: whole blood 9


title: CTL_M_27

description: normal blood sample

source_name: whole blood 14


title: BR099

source_name: Primary Tumor

value: Primary Tumor

value: early


title: siC vs siD Replicate 2

city: Taipei

first: Hung-Hsi

last: Chen

address: N223, IBMS, No. 128, Sec. 2, Academia Rd.

country: Taiwan

institute: Academia Sinica

description: Biological replicate 2 of 2

hyb_protocol: 0.3 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to an Agilent array (Agilent Technologies, USA) at 65°C for 17 h

scan_protocol: Arrays were scanned on Agilent Technologies Scanner G2505C, and mages were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: SAS tongue squamous cell carcinoma cell lines_siControl

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.3 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: SAS cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) fetal bovine serum at 37°C with a humidified atmosphere of 5% CO2.

extract_protocol: RNA was extracted by using Trizol (ThermoFisher) and then purified by using RNeazy mini kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: SAS cells were transfected with siRNA for 48 hours

tag: cell line

value: SAS

tag: treatment

value: siC transfection

source_name: SAS tongue squamous cell carcinoma cell lines_siDDX3

value: siD transfection


title: siC vs siD Replicate 1

description: Biological replicate 1 of 2


title: H26_stationary

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

description: Non replicating sample of H26 wild type strain

data_processing:
Reads were mapped to the reference genome NC_013967
Samtools view was used to filter reads, retaining uniquely mapped reads with each segment properly aligned according to the aligner (-f 2) and with high mapping quality (-q 50).
Replication timing profiles were generated by normalizing the replicating (log phase) sample to the non-replicating (stationary) sample in 1 kb windows.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor.
Genome_build: Haloferax volcanii NC_013967
Supplementary_files_format_and_content: Processed files (*.bed)

organism: Haloferax volcanii

source_name: exponentially growing cells

growth_protocol: Cells were harvested from early-log phase cultures grown in YPC media.

extract_protocol:
Genomic DNA was extracted by spooling: cells were resuspended in ST buffer (1 M NaCl, 20 mM Tris.HCl) and then lysed in lysis solution lysis solution (100 mM EDTA pH 8.0, 0.2% SDS). Aqueous layer was overlayed with 1 ml ethanol, and DNA was spooled at teh interface. DNA was phenol-chloroform precipitated for 2 times.
Library preparation and sequencing was carried out according to Illumina instructions.

tag: strain

tag: relevant genotype

value: laboratory strain, Wild type


title: BR097

tag: cell type

tag: ihc


title: H2202_log

description: Replicating sample of H2202 orc3 orc5 mutant strain

value: H2202 orc3 orc5

value: orc5 orc3 deletion mutant


title: BRD4_ChIPseq_1c

description:
0007Ohio_CLL_BRD4_2nd_actregs.xlsx
03_0007Ohio_CLL_Patient_1c_BRD4_hs_i85

source_name: B-Chronic Lymphocytic Leukemia (CLL) cels

value: 4 hours stimulation with 3.2uM of CpG oligonucleotide + 1 uM of BET inhibitor (PLX51107)

value: BRD4 (Active Motif #A301-985A1)


title: Sexual 1.1

source_name: Square regions directly below cephalic ganglia

tag: tissue


title: Sexual 1.3

source_name: Square region from below pharynx to below gonopore


title: Brain 2

description:
processed data file:
BrainClusteringDigitalExpressionMatrix.dge.txt

source_name: Square surrounding eyes and extending three eye-lengths below eyes

value: No X1


title: P5_M_ICF1_22

description: ICF1 blood sample

source_name: whole blood 6


title: BR091

value: TN

value: pre


title: H1689_log

description: Replicating sample of H1689 orc5 mutant strain

value: orc5 deletion mutant


title: Brain 1

source_name: Square directly below eyes, enriched for ventral half


title: BR065

value: late

value: ER+


title: H26_log

description: Replicating sample of H26 wild type strain


title: BRD4_ChIPseq_1a

description:
0007Ohio_CLL_BRD4_2nd_actregs.xlsx
01_0007Ohio_CLL_Patient_1a_BRD4_hs_i79

value: Primary B-CLL cells

value: baseline


title: Trunk 3

description:
processed data file:
PrincipalClusteringDigitalExpressionMatrix.dge.txt

source_name: Trunk (region above pharynx reaching below pharynx. Pharynx was removed)


title: BRD4_ChIPseq_1b

description:
0007Ohio_CLL_BRD4_2nd_actregs.xlsx
02_0007Ohio_CLL_Patient_1b_BRD4_hs_i82

value: 4 hours stimulation with 3.2uM of CpG oligonucleotide


title: BR052

description:
expression_tpm.txt
The raw data were submitted to EGA
EGA study accession: EGAS00001002621
https://www.ebi.ac.uk/ega/studies/EGAS00001002621

value: Primary Tumor


title: BR088

value: early


title: Pre-pharyngeal 2.2

source_name: Pre-pharyngeal (region below head region and above pharynx)


title: pH_M_ICF1_23

description: ICF1 blood sample

source_name: whole blood 5

value: Male

value: Whole blood


title: pY_M_ICF1_17

description: ICF1 blood sample

source_name: whole blood 4


title: BRD4_ChIPseq_3a

description:
0086Ohio_CLL_BRD4_actregs.xlsx
01_01UG_0086Ohio_3a-vehicle_BRD4_hg19_i79


title: Pre-pharyngeal 2.1

value: Pre-pharyngeal (region below head region and above pharynx)


title: BR105


title: LD_ZT14_A (XR-seq)

source_name: LD_ZT14, whole plant

tag: ecotype

tag: experiment

tag: time

value: seedlings


title: LD_ZT11_A (XR-seq)

source_name: LD_ZT11, whole plant


title: Pharynx 3

source_name: Pharynx (isolated pharynx)

value: Pharynx (isolated pharynx)


title: BR081

source_name: Primary Tumor


title: BR080


title: Trunk 2.2

value: Trunk (region above pharynx reaching below pharynx. Pharynx was removed)


title: LD_ZT5_A (XR-seq)

source_name: LD_ZT5, whole plant


title: CTL_F_2

description: normal blood sample

source_name: whole blood 1

tag: gender

value: Female

value: normal


title: LD_ZT8_A (XR-seq)

source_name: LD_ZT8, whole plant


title: BR090

value: pre


title: Trunk 2.1

value: No X1


title: Head 5.3

source_name: Head (region from head tip to below auricles)


title: LD_ZT2_A (XR-seq)

source_name: LD_ZT2, whole plant


title: CTL_M_4

description: normal blood sample

source_name: whole blood 2

tag: disease state


title: BR089

value: late


title: Head 5.2

value: Head (region from head tip to below auricles)


title: Head 5.1


title: CTL_M_5

description: normal blood sample

source_name: whole blood 3


title: LD_ZT17_A (XR-seq)

source_name: LD_ZT17, whole plant


title: Control Mature B Cells vs. Notch1-Activated Mature B Cells

city: Kyoto

first: Hiroshi

last: Arima

address: 54 Shogoin Kawahara-cho, Sakyo-ku

department: Department of Hematology and Oncology

country: Japan

institute: Graduate School of Medicine, Kyoto University

description: Equal amounts of total RNA from 3 mice per group were pooled together.

hyb_protocol: 300 ng of Cy3-labeled cRNA and same amount of Cy5-labeled one were mixed and fragmented at 60°C for 30 minutes using Gene Expression Hybridization Kit (Agilent Technologies) in a reaction volume of 25 μL containing 1× fragmentation buffer and 2× blocking agent, and the sample was applied to Agilent SurePrint G3 Mouse 8x60K v2 microarray following manufacturer's instructions. After hybridization, the slide was washed sequentially with Agilent Gene Expression Wash Buffer.

scan_protocol: The slide was scanned on an Agilent G2505C Microarray Scanner (scan resolution, 3 μm; TIFF file dynamic range, 20 bit).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and lowess normalization.

source_name: Control mature B cells

label_protocol: Cy3- and Cy5-labeled cRNA was prepared from 50 ng total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA) and purified using Rndasy mini spin columns (Qiagen) following manufacturer's instructions

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) following manufacturer's instructions.

treatment_protocol: Control mature B cells and Notch1-activated ones were sorted for CD19+ RFP+ splenocytes from 3-month-old Aicda-Cre Tg/- Rosa26-reporter RFP KI/WT mice and Aicda-Cre Tg/- conditional NICD1 Tg/- Rosa26-reporter RFP KI/WT mice, respectively. Both mice were on a mixed B6 × MCH(ICR) genetic background.

tag: strain background

value: mixed B6 × MCH(ICR)

value: splenic mature B cells

tag: age

value: 3 months

tag: genotype

value: control

source_name: Notch1-activated mature B cells

tag: background strain


title: BR077

value: Primary Tumor

value: early

value: ER+


title: LD_ZT23_A (XR-seq)

source_name: LD_ZT23, whole plant


title: LD_ZT20_A (XR-seq)

source_name: LD_ZT20, whole plant


title: BR084


title: Pharynx 2

tag: strain/cell line

tag: facs gate

value: All Cells

tag: drop-seq run number (per biological sample)


title: BR078

value: TN


title: BR079


title: Head 4.3


title: BR064


title: Pharynx 1

value: Pharynx (isolated pharynx)


title: Input

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: WT

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 software.
For peak callling, MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files that we uploaded are MACS2 called peak files of WT and DR8dex2 hMSCs. And, all of the processed data files are xls format.

source_name: Mesenchymal stem cell

growth_protocol: Human MSCs (hMSCs) derived from hESCs and primary human MSCs were cultured in MEM (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/mL bFGF (Joint Protein Central, JPC).

extract_protocol:
DNA was isolated using phenol-chloroform-isoamylalcohol extraction and ethanol precipitation.
The H3K9me3 enriched fragments were contructed into libararies via KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series(KK8504) following the manuals.

value: ES-derived  mesenchymal stem cell

value: WT

tag: passage


title: ChIP-seq_DR8dex2_rep1

description:
DR8dex2
DR8dex2_peaks.xls


title: ChIP-seq_WT_ rep2

description:
WT
WT_peaks.xls


title: ChIP-seq_DR8dex2_rep2

description:
DR8dex2
DR8dex2_peaks.xls


title: Head 4.4


title: BR029


title: Head 4.2


title: Head 4.1


title: BR038


title: BB01_055_N

source_name: Adjacent Normal

value: Adjacent Normal Cells


title: Tail 1.2

source_name: Tail (region below pharynx to tail tip)

value: Tail (region below pharynx to tail tip)


title: BB01_044_N


title: BB01_049_N


title: Tail 1.1


title: BB01_030_N


title: Trunk 1.2

source_name: Trunk (region above pharynx reaching below pharynx. Pharynx was removed)


title: BB01_032_N


title: BB01_028_N


title: Pre-pharyngeal 1.2

source_name: Pre-pharyngeal (region below head region and above pharynx)


title: Trunk 1.1

value: Trunk (region above pharynx reaching below pharynx. Pharynx was removed)


title: sqWAT-MSC, Gata2 over expression rep2

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine (MDC)

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99 C for 5 min and hybridized for 16h at 45 C to Mouse Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100 mM MES, 0.1 M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Probe intensity (.cel) data was normalized using RMA as implemented in Partek Genomics Suite (v6.6, Partek, Inc., St. Louis, MO).

label: biotin

source_name: sqWAT-MSC

label_protocol: 100 ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling

growth_protocol: Freshly isolated cells were seeded in 6 well plates and maintained in DMEM with 10% FBS, 1% Pen/Strep (all ThermoFisher), and 10 mM HEPES. Cells were cultivated for at least 2 passages before inducing differentiation. MSC identity was analyzed by FACS.

extract_protocol: Isolation and maintenance of sqWAT-derived MSCs was performed as described elsewhere (Siersbæk, M. S. et al. Genome-wide profiling of peroxisome proliferator-activated receptor γ in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression. Mol. Cell. Biol. 32, 3452–3463 (2012).). In short, male C57Bl/6J mice aged 8-12 weeks were sacrificed and sqWAT isolated. The tissue was cut into small pieces, digested with collagenase, type II (Sigma), and filtered through a 70 µm mesh to obtain sqWAT MSCs.

treatment_protocol: For differentiation, cells were seeded in 24 or 48 well plates and grown to ~80% confluency. Ostoblastogenesis was induced by 10 mM ß-glycerophosphate, 50 µg/ml ascorbic acid and 50 ng/ml BMP-2 and culture medium changed every other day.The coding sequences of murine GATA2 sequence was cloned downstream of a Kozak consensus into a pMSCV vector containing a puromycin resistance cassette (Takara Clontech) and verified by sequencing. EcoPack 2-293 cells (Takara Clontech) were transfected with GATA2 or empty pMSCV vectors using Lipofectamine 2000 (ThermoFisher). The retroviral particles-containing media was harvested 48 hours later. The supernatants were supplemented with 10 µg/ml polybrene and used to infect pre-confluent C3H10T1/2 or primary sqWAT-derived MSCs for 24 hours. 48 hours later, cells were cultured in the presence of 1 µg/ml puromycin.

tag: strain

value: sqWAT-MSC Gata2 over-expression


title: BB01_020_N

tag: cell type


title: Pre-pharyngeal 1.1

value: Pre-pharyngeal (region below head region and above pharynx)


title: sqWAT-MSC, Gata2 over expression rep1


title: ChIP-seq_WT_ rep1

description:
WT
WT_peaks.xls


title: sqWAT-MSC, Gata2 over expression rep3


title: Head 3

value: Head (region from head tip to below auricles)


title: BB01_005_N

tag: ihc


title: BB01_012_N


title: Head 2

tag: tissue


title: BB01_004_N


title: Head 1


title: sqWAT-MSC, Control rep3

value: sqWAT-MSC control


title: sqWAT-MSC, Control rep2


title: Whole animal 1.1

source_name: Whole animal

value: Whole animal


title: sqWAT-MSC, Control rep1


title: M5487

status: Public on Apr 16 2018

city: Hanover

first: Günter

last: Bernhardt

address: Carl Neuberg Strasse 1

department: Institue of Immunology

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 300ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per probe and sample. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by quantile normalization first, followed by global linear scaling. For this latter approach, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 20. All of those normalized gPS values that fell below this intensity border were substituted by the respective surrogate value of 20.

source_name: TFR (GL7+/-, immunisation, pLN, d25)

label_protocol: 40 to 50 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as directed by the company (applying one-round of amplification), except that reaction volumes were halved. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies). Prior to the reverse transcription reaction, 1µl of a 1:100000 dilution of Agilent’s ‘One-Color spike-in Kit stock solution’ (#5188-5282, Agilent Technologies) was added to a subset of total RNA sample.

extract_protocol: Total RNA was extracted by use of the RNeasy Micro Kit (Qiagen).

value: perpheral lymph node

value: follicular T regulatory (TFR)

value: mixed, 8-15 mice

value: 8-14 weeks

tag: rna input amount

value: 40 ng


title: M5325

source_name: TFH (GL7+, peyer's patches)

value: Peyer's Patches

value: follicular T helper (TFH)


title: M5327

source_name: Treg (peyer's patches)

value: regulatory T cells (Treg)


title: M5482

source_name: Treg (immunisation, pLN, d12)


title: M5484

source_name: Tnaive (immunisation, pLN, d25)

value: naive T


title: M5483

source_name: TFR (GL7+/-, immunisation, pLN, d12)


title: M5217

value: 50 ng


title: M5215


title: M5326

source_name: TFH (GL7-, peyer's patches)


title: LH3-AL-5

city: beijing

first: li

last: Michael

address: beiqing road

institute: Basepedia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using STAR v2.5.1b_modified with parameters --outQSconversionAdd 0 --runThreadN 4 -twopassMode Basic --quantMode - --alignSoftClipAtReferenceEnds No  --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical  --outSAMmapqUnique 254
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
Brain were collected for isolation of cerebral vessels. Briefly, mice were transcardially perfused with ice-cold phosphate-buffered saline. Then, brains were removed, rinsed in cold isotonic sucrose buffer (0.32 mol/L sucrose, 3 mmol/L HEPES, pH 7.4), cleared of pia mater and choroid plexus. The brain was homogenized with a tight fitting pestle Dounce homogenizer in 5 ml of sucrose buffer. The homogenate was centrifuged at 1000g for 10 min. The supernatant containing neuronal cells was discarded and the white layer of myelin in the upper part of the pellet was removed. The pellet was resuspended again in 5 ml of the same cold buffer and centrifuged at 1000g for another 10 min. We repeated the washes three times to eliminate the rest of the myelin and free neurons. The pellet was resuspended in 3 ml of the sucrose buffer and centrifuged at 350g to eliminate detached cells. This step was repeated three times and the resulting pellet was resuspended in 1 ml of sucrose buffer and centrifuged at 75g for 5 min. The resulting supernatant was used as the cerebral vessels preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8 months old

value: Wild type

tag: treatment

value: stereotactic injection of AAV-LH3 and treated with AngII plus L-NAME

value: cerebral vessels


title: M5486

source_name: Treg (immunisation, pLN, d25)


title: LH3-AL-4


title: LH3-AL-3


title: M5328

source_name: TFR (GL7+/-, peyer's patches)


title: M5480

source_name: Tnaive (immunisation, pLN, d12)


title: M5218


title: M5141


title: M5140


title: M5216


title: M5138


title: BMDM_RNA_0hKLA_rep1

city: Piscataway

first: Jia

last: Fei

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University - New Brunswick

data_processing:
Human ChIP-seq sequencing data were aligned to the hg19 reference genome by using Bowtie, PCR duplicates were removed with the Picard tool
Human RNA-seq sequencing data were aligned to the hg19 reference genome by using the STAR RNA-seq aligner, PCR duplicates were removed with the Picard tool. Reads were assigned to genes and were anlyzed by using featureCounts V1.5.3. DESeq2 package was used to analyze gene expression levels.
Mouse sequencing data were aligned to the mm10 genome by using Bowtie2, and all data were analyzed with HOMER.
Human GRO-seq sequencing data were aligned to the hg19 genome by using Bowtie2, and all data were analyzed with HOMER.

growth_protocol: Human Cells were maintained in DMEM with 10% FBS, 5% CO2, 37oC. Mouse BMDMs were generated from bone marrow and cultured in DMEM supplemented with M-CSF for 7 days and activated with KLA as descried.

extract_protocol:
For human ChIP-seq, ~15 million wild-type HeLa S3 cells or the indicated hNDF knockout cells were collected and crosslinked with 1% formaldehyde. After cell lysis and genome fragmentation by sonication, samples were incubated with 20 ?L of Dynabeads Protein A that were pre-bound with 1 ?L of NDF antiserum. [Note that 1 ?L of hNDF antiserum was optimal for hNDF antiserum #7. For hNDF antiserum #6, 2 ?L was the optimal volume.] Bound DNA were isolated with MinElute columns (Qiagen). For human RNA-seq, total RNA was purified by using the PureLink RNA Mini RNA Kit (Thermo Fisher Invitrogen). Mouse BMDM ChIP-seq and RNA-seq were performed as described in Kaikkonen, M. U. et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell 51, 310-325.
Human ChIP-seq libraries were prepared by end-repair, A-tailing, and ligation of Illumina TruSeq adaptors, which was then followed by PCR amplification and size selection with AMPure beads (Beckman Coulter). Human RNA-seq libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Mouse ChIP-seq libraries were prepared from ChIP DNA and inputs by blunting, A-tailing, and adapter ligations were performed by using NextFlex barcode adapters. Mouse RNA-seq libraries were prepared from poly(A)-enriched mRNA, as described in Kaikkonen, M. U. et al. Mol. Cell 51, 310-325. GRO-seq libraries were prepared using NEBNext multiplex small RNA library prep set for Illumina.

treatment_protocol: Mouse BMDM were trated with KLA as indicated.

value: C57BI/6 (Harlan Laboratories)

value: 8-10 weeks

tag: Sex

value: female

value: Primary BMDM

tag: genotype/variation

value: WT

tag: chip antibodies


title: BMDM_RNA_6hKLA_rep1


title: BMDM_RNA_0hKLA_rep2


title: BMDM_ChIP_NDF7_6hKLA

description:
BMDM_ChIP_NDF7_6hKLA
processed data file:
diffNDF7regions_F8_6hKLA_vs_notx.bed
diffNDF7regions_F8_6hKLA_vs_notx.txt

value: NDF7, home-made


title: BMDM_ChIP_NDF7_0hKLA

description:
BMDM_ChIP_NDF7_0hKLA
processed data file:
diffNDF7regions_F8_6hKLA_vs_notx.bed
diffNDF7regions_F8_6hKLA_vs_notx.txt


title: M5139

source_name: TFH (GL7+, immunisation, pLN, d12)

value: perpheral lymph node

tag: gender

value: mixed, 8-15 mice

value: 8-14 weeks


title: LH3-AL-2

tag: age


title: BMDM_RNA_6hKLA_rep2


title: M5481

value: follicular T helper (TFH)

value: 40 ng


title: LH3-AL-1

tag: genotype


title: M5485

source_name: TFH (GL7+, immunisation, pLN, d25)


title: BMDM_ChIP_input_0hKLA


title: GFP-AL-5

source_name: GFP-AL

value: stereotactic injection of AAV-GFP and treated with AngII plus L-NAME


title: BMDM_ChIP_H3K36me3_6hKLA

value: Abcam, ab9050


title: BMDM_ChIP_H3K36me3_0hKLA


title: GFP-AL-2

value: 8 months old


title: GFP-AL-1

value: Wild type


title: GFP-Veh-5

source_name: GFP-Veh

value: stereotactic injection of AAV-GFP and treated with saline


title: GFP-Veh-4

value: cerebral vessels


title: HeLa Clone KO1.2, RNA-seq, rep 1

source_name: HeLa S3 NDF knockout 1.2

value: HeLa S3

value: NDF knockout 1.2

tag: molecule

value: total RNA


title: HeLa Clone KO1.1, RNA-seq, rep1

source_name: HeLa S3 NDF knockout 1.1

value: NDF knockout 1.1


title: HeLa Clone KO1.1, GRO-seq

value: BrdU antibody, sc-32323 AC, Santa Cruz

value: nascent RNA


title: HeLa WT, GRO-seq

source_name: HeLa S3 WT

value: WT


title: GFP-Veh-2


title: HeLa Clone KO1.2, GRO-seq


title: GFP-AL-3


title: GFP-Veh-1


title: HeLa Clone KO1.2, anti-NDF 7-rep2 ChIP-seq

source_name: HeLa Clone KO1.2, anti-NDF 7

value: NDF7, home-made


title: HeLa Clone KO1.2, anti-NDF 7-rep1 ChIP-seq


title: HeLa Clone KO1.2, anti-NDF 6-rep4 ChIP-seq

source_name: HeLa Clone KO1.2, anti-NDF 6

value: NDF6, home-made


title: HeLa WT, RNA-seq, rep1


title: GFP-AL-4


title: BMDM_ChIP_input_6hKLA

value: C57BI/6 (Harlan Laboratories)

value: 8-10 weeks

value: female

value: Primary BMDM


title: HeLa Clone KO1.2, anti-NDF 6-rep2 ChIP-seq


title: P7802_242 Mac_WT

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

data_processing:
Clustering was done by 'onboard clustering' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq Rapid SBS Kit v2' chemistry.
The Bcl to FastQ conversion was performed using bcl2fastq from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm8 whole genome using STAR in the scilifelab NGI-RNAseq nextlow pipeline
https://github.com/SciLifeLab/NGI-RNAseq
Genome_build: GRCm38
Supplementary_files_format_and_content: ; seperated csv file include Dseq2 normalized counts for every sample

source_name: Macrophages

extract_protocol:
Sorting strategy: Dead–Ly6C–CD11b+F4/80lo (WT) or Dead–Ly6C–CD11b+F4/80hi (Tgfbr2 KO). Three biological samples were sorted per group where each sample was a pool of 1-5 mice. Cells were lysed in RLT+beta-mercaptoethanol and RNA was isolated using RNeasy Micro kit. RNA integrity and concentration was assessed using Bioanalyzer 2100 (Agilent). Each sample had RIN 7.1-10 and input amount was >100 pg RNA/sample.
RNA libraries were prepared for sequencing using the SMARTer Stranded Total RNA-seq Kit - Pico Input Mammalian (Clontech).

treatment_protocol: For microglia, Tgfbr2fl/fl (WT) or Cx3cr1CreER/+Tgfbr2fl/fl (Tgfbr2 KO) mice were injected subcutaneously with tamoxifen (three daily injections of 5mg) and microglia were sorted from brains and spinal cords 18-22 days later. For monocyte-derived macrophages, Cx3cr1CreER/+R26DTA/+ were irradiated and transplanted with Tgfbr2fl/fl (WT) or Cx3cr1CreER/+Tgfbr2fl/fl (Tgfbr2 KO) bone marrow. After 6 weeks, mice were given tamoxifen (as above) to deplete microglia. The CNS repopulating monocyte-derived macrophages were sorted 18-22 days later.

tag: knockout status

tag: lane


title: P7802_218 Mac_KO

value: Tgfbr2 KO


title: P7802_226 Mac_KO


title: P7802_250 Mac_WT


title: P7802_234 Mac_WT


title: HeLa Clone KO1.2, anti-NDF 6-rep1 ChIP-seq


title: P7802_210 uG_KO

source_name: Microglia


title: GFP-Veh-3

value: 8 months old

value: Wild type


title: P7802_202 uG_WT


title: HeLa WT, anti-NDF 7-rep4 ChIP-seq

source_name: HeLa WT, anti-NDF 7


title: HeLa Clone KO1.2, anti-NDF 7-rep4 ChIP-seq


title: P7802_157 uG_KO


title: HeLa WT, anti-NDF 7-rep2 ChIP-seq


title: HeLa WT, anti-NDF 7-rep1 ChIP-seq


title: P7802_149 uG_KO


title: P7802_141 uG_WT


title: P7802_117 Mac_KO


title: HeLa WT, anti-NDF 6-rep1 ChIP-seq

source_name: HeLa WT, anti-NDF 6


title: HeLa WT, anti-NDF 6-rep4 ChIP-seq


title: HeLa WT, anti-NDF 6-rep2 ChIP-seq


title: P7802_133 uG_WT


title: 1_S57_20:00

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

description:
Biopsy from subject 1 at time (h) 20:00
norm_reads_count.txt

data_processing:
Demultiplexing was done using bcl2fastq software
Paired-end reads were mapped to the Homo sapiens genome (GRCh38/hg38) using STAR (Dobin et al. 2013) with parameters “—alignIntronMin 20 –alignIntronMax 1000000 – GTF (option –sjdbGTFfile) and adapter clipping.
Mapped reads were quantified in intronic and exonic regions. For each gene, we defined a gene body by merging all the respective transcripts using BEDtools (Quinlan and Hall 2010). A region was defined as exonic if it occurs in a least one of the transcripts while an intronic region had to be shared between all the transcripts. We assigned uniquely mapping paired-reads to exonic regions (exon/exon and complete exon reads) or intronic regions (intron-exon and complete intron reads) considering reads orientation.
Intronic and exonic reads count were normalized using EdgeR (Robinson et al. 2010) by the library scaling factor from the exonic regions and the respective intronic and exonic length (rpkm()).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample at the pre-mRNA and mRNA levels (introns, exons).

source_name: biopsys  from the vastus lateralis

growth_protocol: 10 healthy volunteers were recruited for the in vivo study (see Table S1 for donor characteristics). One week prior to the scheduled laboratory visit, participants had to adhere to a consistent daily feeding and sleeping routine. Participants arrived in the laboratory at 19:00 h on the day prior to the testing day and ingested one standardized meal that first evening. Participants remained for the duration of their stay in a semi-recumbent position. During the waking hours of the testing day they were given mixed-macronutrient meal-replacement solutions at hourly intervals (Resource, Nestlé, CH) to ensure energy balance. The laboratory was free from natural light and with artificial lighting standardized to 800 lux in the direction of gaze, ambient temperature maintained between 20-25°C and noise levels tightly regulated. Participants were not permitted to sleep during waking hours when lights were on (i.e. 07:00-22:00 h) and wore eye masks whilst trying to sleep during lights-out (i.e. 22:00-07:00 h)

extract_protocol:
Six 100 mg biopsy samples were acquired from the vastus lateralis muscle at 4-hour intervals (12:00, 16:00, 20:00, 24:00, 04:00 & 08:00 h) and immediately snap frozen under liquid nitrogen. Samples were taken from each leg in alternating and ascending order with skin incisions separated by 2-3 cm
Sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded Total LT Sample Prep Kit (Illumina) with the Ribo-Zero Gold depletion set

treatment_protocol: Anesthetic administration (1% lidocaine w/o epinephrine) and skin/fascia incisions for this procedure (Bergstrom 1962) were completed within the hour prior to sleep such that night-time samples could be acquired with minimal discomfort.

value: vastus lateralis

tag: time


title: 1_S56_16:00

description:
Biopsy from subject 1 at time (h) 16:00
norm_reads_count.txt


title: 12_S54_08:00

description:
Biopsy from subject 12 at time (h) 08:00
norm_reads_count.txt


title: 1_S55_12:00

description:
Biopsy from subject 1 at time (h) 12:00
norm_reads_count.txt


title: 1_S59_04:00

description:
Biopsy from subject 1 at time (h) 04:00
norm_reads_count.txt


title: 1_S58_00:00

description:
Biopsy from subject 1 at time (h) 00:00
norm_reads_count.txt


title: 1_S60_08:00

description:
Biopsy from subject 1 at time (h) 08:00
norm_reads_count.txt


title: 12_S52_00:00

description:
Biopsy from subject 12 at time (h) 00:00
norm_reads_count.txt


title: 12_S50_16:00

description:
Biopsy from subject 12 at time (h) 16:00
norm_reads_count.txt


title: 12_S49_12:00

description:
Biopsy from subject 12 at time (h) 12:00
norm_reads_count.txt


title: 4_S48_08:00

description:
Biopsy from subject 4 at time (h) 08:00
norm_reads_count.txt


title: 4_S45_20:00

description:
Biopsy from subject 4 at time (h) 20:00
norm_reads_count.txt


title: Brain_Pofut1FloxControl_rep2

city: Columbus

first: Paul

middle: T

last: Martin

address: 700 Childrens Dr.

department: Center for Gene Therapy

institute: Nationwide Childrens Hospital

hyb_protocol: For each array, 2.2 µg of fragmented and labeled cDNA was hybridized onto 430 2.0 GeneChips® (Affymetrix Inc., USA), for 16 hours at 45°C followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA).

data_processing:
CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) (Affymetrix Inc., USA) and probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene).
Probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and differential gene expression was determined by pair-wise comparisons.

source_name: Brain, Flox control

label_protocol: The OvationTM Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc.; San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from 25ng of total RNA from Brain tissue following manufacturer's protocol.

growth_protocol: All mice were maintained in the animal facility of the Research Institute of Nationwide Childrens Hospital following the IACUC guidelines.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's protocol followed by purification on a silica-gel-based membrane (Rneasy-Mini; Qiagen, Valecia, CA).

value: 2 months

value: Brain


title: Brain_Pofut1KnockOut_rep1

source_name: Brain, Pofut1 Knockout


title: Brain_NestinCreControl_rep1

source_name: Brain, NestinCre control


title: Brain_Pofut1KnockOut_rep2


title: 4_S44_16:00

description:
Biopsy from subject 4 at time (h) 16:00
norm_reads_count.txt


title: 4_S43_12:00

description:
Biopsy from subject 4 at time (h) 12:00
norm_reads_count.txt


title: Brain_Pofut1FloxControl_rep1


title: Brain_NestinCreControl_rep2


title: 4_S46_00:00

description:
Biopsy from subject 4 at time (h) 00:00
norm_reads_count.txt


title: 4_S47_04:00

description:
Biopsy from subject 4 at time (h) 04:00
norm_reads_count.txt


title: 13_S39_20:00

description:
Biopsy from subject 13 at time (h) 20:00
norm_reads_count.txt


title: 13_S41_04:00

description:
Biopsy from subject 13 at time (h) 04:00
norm_reads_count.txt


title: 13_S40_00:00

description:
Biopsy from subject 13 at time (h) 00:00
norm_reads_count.txt


title: 13_S38_16:00

description:
Biopsy from subject 13 at time (h) 16:00
norm_reads_count.txt


title: 13_S37_12:00

description:
Biopsy from subject 13 at time (h) 12:00
norm_reads_count.txt


title: 12_S53_04:00

description:
Biopsy from subject 12 at time (h) 04:00
norm_reads_count.txt


title: 12_S51_20:00

description:
Biopsy from subject 12 at time (h) 20:00
norm_reads_count.txt


title: 9_S31_12:00

description:
Biopsy from subject 9 at time (h) 12:00
norm_reads_count.txt


title: 9_S34_00:00

description:
Biopsy from subject 9 at time (h) 00:00
norm_reads_count.txt


title: 9_S33_20:00

description:
Biopsy from subject 9 at time (h) 20:00
norm_reads_count.txt


title: 9_S36_08:00

description:
Biopsy from subject 9 at time (h) 08:00
norm_reads_count.txt


title: 13_S42_08:00

description:
Biopsy from subject 13 at time (h) 08:00
norm_reads_count.txt


title: 9_S32_16:00

description:
Biopsy from subject 9 at time (h) 16:00
norm_reads_count.txt


title: 9_S35_04:00

description:
Biopsy from subject 9 at time (h) 04:00
norm_reads_count.txt


title: 7_S27_20:00

description:
Biopsy from subject 7 at time (h) 20:00
norm_reads_count.txt


title: 7_S25_12:00

description:
Biopsy from subject 7 at time (h) 12:00
norm_reads_count.txt


title: 7_S26_16:00

description:
Biopsy from subject 7 at time (h) 16:00
norm_reads_count.txt


title: 6_S23_04:00

description:
Biopsy from subject 6 at time (h) 04:00
norm_reads_count.txt


title: 6_S21_20:00

description:
Biopsy from subject 6 at time (h) 20:00
norm_reads_count.txt


title: 6_S20_16:00

description:
Biopsy from subject 6 at time (h) 16:00
norm_reads_count.txt


title: 6_S19_12:00

description:
Biopsy from subject 6 at time (h) 12:00
norm_reads_count.txt


title: 2_S17_04:00

description:
Biopsy from subject 2 at time (h) 04:00
norm_reads_count.txt


title: 2_S15_20:00

description:
Biopsy from subject 2 at time (h) 20:00
norm_reads_count.txt


title: ∆treR trehalose replicate 2

city: Rochester

first: Roberta

middle: C

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

data_processing:
Barcodes were trimmed, low quality and short sequences (<100bp) were filtered using BBDuk (https://sourceforge.net/projects/bbmap) implemented in Geneious version 11 (https://www.geneious.com).
Expression values for each mRNA sample were generated by mapping of paired reads onto the annotated reference genome of S. mutans UA159 resulting in 175 to 275X mean coverage per sample (range of 4.2 to 6.4M reads mapped per sample).
Expression level counts and differential expression calculations in triplicate between conditions were performed using Geneious version 11 (https://www.geneious.com) using DESeq2 normalization. DESeq2 uses a model based on the negative binomial distribution with variance and mean linked by local regression (36).
Genome_build: Streptococcus mutans UA159
Supplementary_files_format_and_content: treR_RNAseq Processed data.xlsx:  Excel file containing the output prior to statistical analysis from all of the samples (UA159 vs. ∆treR) for each gene in the genome

organism: Streptococcus mutans

source_name: Streptococcus mutans ∆treR strain

growth_protocol: all strains of Streptococcus mutans were grown to mid-log phase in TY medium supplemented with the indicated sugar at 37˚C in a 5%(v/v) CO2/95% air atmosphere

extract_protocol:
RNA extraction was performed using the Qiagen RNeasy Power Microbiome Kit according to the manufacturer's instructions, mRNA was purified using the Zymo RNA Clean and Concentrator Kit
cDNA libraries from rRNA-depleted RNA were generated using random-primed cDNA synthesis methods according to the ScriptSeq v2 RNASeq Library preparation protocol (Epicentre, Madison, WI).  Prior to second strand cDNA synthesis, the di-tagged cDNA was purified using the Agencourt AMPure XP system (Beckman Coulter, Brea, CA).  ScriptSeq index primers were added to the libraries which were then PCR amplified for 15 cycles.

tag: growth media

value: delta-treR


title: ∆treR trehalose replicate 3

tag: strain


title: 2_S14_16:00

description:
Biopsy from subject 2 at time (h) 16:00
norm_reads_count.txt


title: 6_S24_08:00

description:
Biopsy from subject 6 at time (h) 08:00
norm_reads_count.txt


title: ∆treR trehalose replicate 1


title: 2_S13_12:00

description:
Biopsy from subject 2 at time (h) 12:00
norm_reads_count.txt


title: 6_S22_00:00

description:
Biopsy from subject 6 at time (h) 00:00
norm_reads_count.txt


title: 3_S12_08:00

description:
Biopsy from subject 3 at time (h) 08:00
norm_reads_count.txt


title: UA159 trehalose replicate 3

source_name: Streptococcus mutans UA159 parent strain

value: wild type


title: UA159 trehalose replicate 2


title: 2_S16_00:00

description:
Biopsy from subject 2 at time (h) 00:00
norm_reads_count.txt


title: UA159 trehalose replicate 1


title: 2_S18_08:00

description:
Biopsy from subject 2 at time (h) 08:00
norm_reads_count.txt


title: 3_S10_00:00

description:
Biopsy from subject 3 at time (h) 00:00
norm_reads_count.txt


title: 3_S9_20:00

description:
Biopsy from subject 3 at time (h) 20:00
norm_reads_count.txt


title: 3_S11_04:00

description:
Biopsy from subject 3 at time (h) 04:00
norm_reads_count.txt


title: ∆treR galactose replicate 3


title: ∆treR galactose replicate 2


title: 3_S8_16:00

description:
Biopsy from subject 3 at time (h) 16:00
norm_reads_count.txt


title: 3_S7_12:00

description:
Biopsy from subject 3 at time (h) 12:00
norm_reads_count.txt


title: 15_S6_08:00

description:
Biopsy from subject 15 at time (h) 08:00
norm_reads_count.txt


title: ∆treR galactose replicate 1


title: wild type mouse MII stage oocytes, biological rep 1

city: La Tronche

first: Christophe

last: Arnoult

address: rond-point de la Chantourne

department: Institute for Advanced Biosciences

institute: INSERM U1209 CNRS UMR5309

description: gene expression data from wild type mouse MII stage oocytes

hyb_protocol: Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 16 hr at 45°C on GeneChip mouse ClariomD arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned with the Affymetrix Genechip Scanner 7G.

data_processing: The data have been normalized with Expression Console from Affymetrix and annotation and analyses have been performed with TAC.3 software from Affymetrix.

source_name: wild type mouse oocytes at MII stage

label_protocol: 250 pg RNA were labeled using the Affymetrix WT pico kit

growth_protocol: Mice were stimulated with 5 UI PMSG and GV oocytes were collected 44 hours later. For MII oocytes, 48 hours after PMSG injection, mice were stimulated with 5 UI HCG and MII oocytes were collected 12 hours later.

extract_protocol: Total RNAs were purified with the Norgen Biotek Corp - Single cell Purification kit following the manufacturer's protocol. The GV samples contained a total of 20 to 32 oocytes; the MII samples a total of 28 to 46 oocytes.

treatment_protocol: Follicular cells were removed by incubating GV or MII oocytes with hyaluronidase (0.1 mg/ml) for 10 min. Remaining follicular attached cells were then removed mechanically with a micropipette. Follicular cell-free oocytes were then collected by aspiration.

value: oocytes, follicular cell free

tag: oocyte stage

value: MII

value: wild type mouse

value: 12 hours post HCG


title: Patl2-KO mouse MII stage oocytes, biological rep 3

description: gene expression data from Patl2-KO mouse MII stage oocytes

source_name: Patl2-KO mouse oocytes at MII stage

value: Patl2-homozygous KO mouse


title: wild type mouse MII stage oocytes, biological rep 2


title: Patl2-KO mouse MII stage oocytes, biological rep 1


title: Patl2-KO mouse GV stage oocytes, biological rep 3

description: gene expression data from Patl2-KO mouse GV stage oocytes

source_name: Patl2-KO mouse oocytes at GV stage

value: GV

value: 44 hours post PMSG


title: F3_BPA_H3K27me3

city: Los Angeles

first: Yen-Wei

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

description: Worms were synchronized by bleaching an adult population of the strain of interest, plating the eggs and allowing the synchronized population to reach L4 larval stage. These were then collected and incubated for 48 hours in 50 µL OP50 bacteria, 500 µL M9 and 0.5 µL of the chemical of interest for a final chemical concentration of 100 µM (DMSO and BPA). After 48 hours, the worms were collected and allowed to recover on NGM plates for 1-2 hours

data_processing:
75-nt reads generated by Illumina sequencing are mapped to the genome using the BWA algorithm with default settings
Peaks were called by MACS2 broadpeak function with q value cutoff = 0.1
Genome_build: ce10
Supplementary_files_format_and_content: bigWig files were generated by using MACS2 signal track building function, scores represent fold enrichment against input and normalized tomillion reads (-SPMR).

organism: Caenorhabditis elegans

source_name: Whole body adult stage

growth_protocol: Worms were maintained on NGM plates streaked with OP50 E. coli and all experiments were performed at 20°C

extract_protocol:
Lysates were obtained from worm body and histone-DNA complexes were isolated with antibody.
Libraries were prepared by Active Motif service

treatment_protocol: Worms were exposed for 48 hours from the L4 stage to 100uM BPA, 0.1% DMSO or water at the P0 generation and collected 24hrs post-L4 at the F3 generation for ChIP-seq experiment

value: BPA 100uM

tag: antibody


title: F3_DMSO_H3K27me3

value: DMSO 0.1%


title: input

description: Worms were synchronized by bleaching an adult population of the strain of interest, plating the eggs and allowing the synchronized population to reach L4 larval stage. These were then collected and incubated for 48 hours in 50 µL OP50 bacteria, 500 µL M9


title: F3_BPA_H3K9me3


title: F3_DMSO_H3K9me3


title: Patl2-KO mouse GV stage oocytes, biological rep 1

tag: tissue


title: 15_S5_04:00

description:
Biopsy from subject 15 at time (h) 04:00
norm_reads_count.txt


title: F3_water_H3K27me3

value: water


title: wild type mouse GV stage oocytes, biological rep 1

description: gene expression data from wild type mouse GV stage oocytes

source_name: wild type mouse oocytes at GV stage


title: 15_S4_00:00

description:
Biopsy from subject 15 at time (h) 00:00
norm_reads_count.txt


title: Patl2-KO mouse MII stage oocytes, biological rep 2


title: Patl2-KO mouse GV stage oocytes, biological rep 2


title: UA159 galactose replicate 1


title: 15_S3_20:00

description:
Biopsy from subject 15 at time (h) 20:00
norm_reads_count.txt


title: F3_water_H3K9me3