title: H3K27ac in confluent Caco2 cells

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie with default parameters
bigWig traces were generated using MACS2 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files containing genomic wiggle traces

source_name: chromatin IP against H3K27ac in confluent Caco2 cells

growth_protocol: for ChIP-seq experiments, Caco-2 cells were grown in 10% FBS DMEM and passaged frequently for subconfluent cells or fed every second day for post-confluent "differentiated" cells. Cells were harvested at 50% confluence (proliferating) or 26 days post-confluent (differentiated)

extract_protocol:
Libraries were constructed using 10 ng each of ChIP and input DNA from up to 3 pooled experiments were processed for deep sequencing according to manufacturer’s instructions (Illumina). Prior to sequencing, qPCR was used to verify that positive and negative control ChIP regions amplified in the linear range.
Libraries were constructed using 10 ng each of ChIP and input DNA from up to 3 pooled experiments were processed for deep sequencing according to manufacturer’s instructions (Illumina).

treatment_protocol: For transcription factor ChIP, cells were fixed in 1% formaldehyde for 10 minutes at 37 degrees, then washed with cold PBS and scraped into PBS, and resuspended in ChIP lysis buffer and immunoprecipitated and processed as described by Carroll, et al, 2005, PMID: 16009131 and as described in our current work. Antibodies used were CDX2 (Bethyl BL3194), GATA6 c-20 (Santa Cruz 7244), GATA6 h-92 (Santa Cruz 9055), HNF4α c-19 (Santa Cruz 6556) or HNF4α h-171 (Santa Cruz 8987). For H3K4me2 ChIP, cells were collected in a digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, 5 mM Na butyrate, complete protease inhibitors) and treated with 0.2 U micrococcal nuclease (MNase, Sigma Aldrich) for 8 min at 37°C. The reaction was terminated by adding 5 mM EDTA in 10 mM Tris, pH7.6, and samples were dialyzed in chromatin RIPA buffer (10 mM Tris, pH7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na deoxycholate, 1% Triton X-100) before overnight IP at 4oC with Histone H3K27Ac (Abcam ab4729) or H3K4Me2 (Millipore 07-030) antibodies. IP material was subsequently handled as described below for conventional ChIP of sonicated genomic DNA.

value: human intestinal cell line

tag: cell line


title: H3K27ac in cycling Caco2 cells

status: Public on May 04 2016

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: chromatin IP against H3K27ac in cycling Caco2 cells

tag: cell type

tag: chip antibody


title: M05226

city: seattle

first: Serge

last: Barcy

state: WA

address: 1900 Ninth Avenue

department: SCRI

institute: Seattle Children's

library_source: transcriptomic

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to alignment to the MneHV7 custom reference genome using TopHat v2.0.12.  Counts were generated from TopHat alignments for each viral gene using the Python package HTSeq v0.6.1 ( http://www-huber.embl.de/users/anders/ HTSeq/doc/overview.html).
Genome_build: custom reference genome from the pigtailed macaque HHV-7 homolog, MneHV7, (GenBank accession number:  KU351741)
Supplementary_files_format_and_content: tab-delimited text files include viral read count values for each sample determined by Htseq using the MneHV7 custom reference genome

molecule: total RNA

organism: Herpesviridae sp.

source_name: salivary gland tissue

extract_protocol:
Salivary gland tissue (parotide gland) were collected and frozen at necropsy.Frozen salivary gland tissue specimens were minced with a sterile razor blade before addition of Trizol. Following a 30 min incubation on ice, total RNA was isolated using a Direct-zol RNA mini prep column (Zymor research) following the manufacturer’s protocol. RNA samples were further purified on “Clean and Concentrate” columns (Zymo research) according to the manufacturer’s instructions. Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences).
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit (Illumina, Inc.) and a Sciclone  NGSx Workstation (PerkinElmer).  Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technology’s Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen).
RNA seq on poly A selected RNA

tag: host

value: Macaca Nemestrina

tag: infection

tag: host tissue

value: parotide

tag: host age

tag: host genotype

value: wild type


title: 366 BN-Oil

city: Kansas City

first: Pramod

last: Dhakal

state: Kansas

address: 3901 Rainbow Boulevard

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

description: barcode: ACTTCC

data_processing:
Base calling by Real-time analysis software (Illumina)
Base call files converted to qseq files by BCL converter (Illumina) and coverted to fastq format for downstream analysis
Reads were mapped to Rat reference genome (Ensembl Rnor_5.0.78) using CLC Bio genmonics workbench 8.0 9 (CLC, Aarhus, Denmark)
Genome_build: Ensembl Rnor_5.0.78
Supplementary_files_format_and_content: Excel (.xls) file containing reads per kilobase per million (RPKM) values

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Uterus

extract_protocol:
RNA extracted by Trizol based protocol
PolyA containing RNA were used to prepare library using TruSeq RNA Sample Preparation Kit (Illumina) acording to manufacturer's guidelines.

treatment_protocol: Progesterone @ 40µg/gm body weight (treatment) and Sesame oil (control) for 9 hours subcutaneously.

tag: tissue

value: uterus

tag: strain

value: Brown Norway (BN)

tag: age

value: 10 weeks

tag: treatment

value: Oil

tag: sampling interval post treatment

value: 9 hour


title: T05183


title: 351 HSD-P4

description: barcode: ACAGTG

value: Holtzman Sprague Dawley (HSD)


title: 357 HSD-P4

description: barcode: ACAGTG


title: M03182


title: K03258


title: 391 HSD-Oil

description: barcode: ACTTGA


title: 332 HSD-P4

description: barcode: ATCACG


title: M03240


title: M02298


title: 336 HSD-Oil

description: barcode: GCCAAT


title: M03126


title: L02393


title: 367 BN-Oil

description: barcode: GTTTCG


title: Patient 47 Tumor

status: Public on May 03 2016

city: Shanghai

first: Gang

last: Liu

address: 320 Yueyang Rd, Shanghai

country: China

institute: Shanghai Institutes for Biological Sciences

data_processing:
quality control
mapping with Tophat2
quantify with Cufflinks
normalization
differential gene analysis with Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: normalized expression level of samples, diffrentially expressed genes between normal and tumor

source_name: Liver

extract_protocol:
Total RNA samples were extracted from snap-frozen tissue sections using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All samples were stored at -80ºC prior to processing.

value: liver

tag: diagnosis

value: Tumor


title: Patient 46 Tumor


title: Patient 49 Tumor


title: Patient 48 Tumor


title: p53-KO

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Chromatin IP against p53.

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1.
Peak-calling by HOMER v4.1.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bedGraph files, HOMER peak output files.

source_name: HCT116 colon cancer cells, p53-KO, p53 ChIP

growth_protocol: Cells were generated by AAV-mediated homologous recombination.

extract_protocol:
Chromatin was sheared by sonication using Bioruptor to an average fragment size of 500 bp, immunoprecipitated using the indicated antibody, purified and sequenced using Illumina HiScanSQ following protocols recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: ATF3-wildtype (ATF3-WT), -knockout (ATF3-KO), p53-knockout (p53-KO) cells were treated with DMSO (Ctrl) or 1.5 uM of camptothecin (CPT) for 4 h, and then crosslinked by 1 mM of di(N-succinimidyl) glutarate (DSG) for 45 min and 1% of formaldehyde for 10 min.

value: colon cancer cell line

tag: genotype/variation

value: DMSO


title: Patient 41 Tumor


title: Patient 45 Tumor


title: Patient 50 Tumor


title: ATF3-Ctrl

description: Chromatin IP against ATF3.

source_name: HCT116 colon cancer cells, ATF3-WT, ATF3 ChIP


title: 337 HSD-Oil

description: barcode: GCCAAT


title: Patient 42 Tumor


title: Patient 40 Tumor


title: Patient 44 Tumor


title: Caki2 expressing PBRM1, Replicate_A

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S University St

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Reads were aligned to hg19 using STAR with the following parameters: readFilesCommand zcat outFilterType BySJout outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterIntronMotifs RemoveNoncanonical
BAM files from STAR were sorted by coordinate.
Gene expression levels were computed using htseq-count using default parameters
Differential expression was performed with DESeq2 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimted text file showing normalized read counts (DESeq normalization method)

source_name: Caki2 cell line, Lentiviral mediated stable expression of PBRM1

growth_protocol: Caki-2 cells (Caki2-Ø as well as Caki2-PBRM1) were cultured in McCoy’s 5A (Corning Mediatech, Inc., Manassas, VA) supplemented with 10% fetal bovine serum (Omega Scientific,Inc, Tarzana, CA), 1% antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin; Corning Mediatech, Inc., Manassas, VA), 1% nonessential aminoacids (Corning Mediatech, Inc., Manassas, VA) and 1% L-glutamine (Corning Mediatech, Inc., Manassas, VA) at 37°C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Doxycycline is added to the culture media at 2µg/ml.

tag: construct

value: doxycycline-inducible lentiviral vector bearing PBRM1

value: stable expression of PBRM1


title: Patient 43 Tumor


title: Patient 39 Tumor


title: M02383


title: Patient 38 Tumor


title: Patient 36 Tumor


title: Patient 37 Tumor


title: Patient 35 Tumor


title: Patient 34 Tumor


title: Patient 33 Tumor


title: pifq hypocotyl dark rep3

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Tair10 whole genome using tophat with parameters -p -r -G -o
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.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: Tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: plant

extract_protocol:
The seeds for RNA-seq were incubated under white light (70 μmol·m-2·s-1) for 3h to trigger germination and treated with FR (2 μmol·m-2·s-1) for 5 min before transfer into darkness. After growth in the dark for four days, the seedlings were harvested or transferred into white light (70 μmol·m-2·s-1) for 1h and 6h. At these time points, the cotyledons and hypocotyls were collected separately for RNA extraction. Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen). mRNA deep sequencing was performed using Illumina HiSeq 2000 (Illumina, Inc., San Diego, CA, USA). Three biological repeats for each sample were prepared for RNA-seq analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hypocotyl

tag: genotype

value: pifq


title: Patient 25 Tumor


title: Patient 26 Tumor


title: pifq hypocotyl dark rep2


title: Patient 31 Tumor


title: Patient 28 Tumor


title: pifq hypocotyl dark rep1


title: Patient 30 Tumor


title: Patient 29 Tumor


title: pifq cotyledon dark rep1

value: cotyledon


title: pifq cotyledon dark rep2


title: wild type hypocotyl dark to light 6h rep1


title: pifq cotyledon dark rep3


title: Patient 24 Tumor


title: Patient 22 Tumor


title: Patient 23 Tumor


title: wild type hypocotyl dark to light 6h rep3


title: wild type hypocotyl dark to light 6h rep2


title: wild type cotyledon dark to light 6h rep3


title: Patient 21 Tumor


title: wild type cotyledon dark to light 6h rep2


title: Patient 32 Tumor


title: wild type cotyledon dark to light 6h rep1


title: Patient 27 Tumor


title: Patient 20 Tumor


title: wild type hypocotyl dark to light 1h rep2


title: wild type hypocotyl dark to light 1h rep3


title: wild type hypocotyl dark to light 1h rep1


title: wild type cotyledon dark to light 1h rep3


title: Patient 19 Tumor


title: wild type cotyledon dark to light 1h rep1


title: wild type cotyledon dark to light 1h rep2


title: wild type cotyledon dark rep3

description: WT_cotyledon_DL1h_D.txt & WT_cotyledon_DL6h_D.txt


title: Patient 15 Tumor


title: wild type cotyledon dark rep2


title: wild type hypocotyl dark rep3

description: WT_hypocotyl_DL1h_D.txt & WT_hypocotyl_DL6h_D.txt


title: Patient 16 Tumor


title: Patient 12 Tumor


title: wild type hypocotyl dark rep2


title: Patient 10 Tumor


title: wild type cotyledon dark rep1


title: Patient 4 Tumor


title: Patient 9 Tumor


title: Patient 17 Tumor


title: wild type hypocotyl dark rep1


title: Patient 18 Tumor


title: Patient 7 Tumor


title: Patient 6 Tumor


title: Patient 3 Tumor


title: Patient 13 Tumor


title: Patient 14 Tumor


title: Patient 5 Tumor


title: Patient 8 Tumor


title: Patient 49 Normal

value: Normal


title: Patient 47 Normal


title: Patient 2 Tumor


title: Patient 11 Tumor


title: Patient 48 Normal


title: Patient 50 Normal


title: Patient 1 Tumor


title: Patient 46 Normal


title: Patient 44 Normal


title: Patient 45 Normal


title: Patient 43 Normal


title: Patient 39 Normal


title: Patient 38 Normal


title: Patient 41 Normal


title: Patient 42 Normal


title: Patient 32 Normal


title: Patient 28 Normal


title: Patient 33 Normal


title: Patient 31 Normal


title: Patient 26 Normal


title: Patient 34 Normal


title: Patient 37 Normal


title: Patient 36 Normal


title: Patient 35 Normal


title: Patient 25 Normal


title: Patient 27 Normal


title: Patient 30 Normal


title: Patient 24 Normal


title: Patient 22 Normal


title: Patient 21 Normal


title: Patient 23 Normal


title: Patient 19 Normal


title: Patient 18 Normal


title: Patient 40 Normal


title: Patient 20 Normal


title: Patient 16 Normal


title: Patient 14 Normal


title: Patient 11 Normal


title: Patient 29 Normal


title: Patient 9 Normal


title: Patient 10 Normal


title: Patient 5 Normal


title: Patient 8 Normal


title: Patient 6 Normal


title: Patient 3 Normal


title: Patient 1 Normal


title: Patient 2 Normal


title: Patient 7 Normal


title: Patient 17 Normal


title: Oocytes, 2-cell and 4-cell embryos

city: Utrecht

first: Siddharth

middle: Subhas

last: Dey

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Fastq files are parsed for library barcodes. Read 1 was mapped to the mm10 build using the Burrows-Wheeler Aligner (BWA), filtered for unique mapping full-length reads and demultiplexed. 5hmCG positions are obtained from the sequencing data using custom scripts in R and Perl identifying CG dinucleotides in the mm10 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request.
Genome_build: mm10
Supplementary_files_format_and_content: Text files with 4 columns: Single Cell ID, chromosome, coordinate and strand (For spikein data, processed data is a text file with 2 columns: counts and unique molecular identifiers)

organism: Mus musculus

source_name: Oocytes, 2-cell and 4-cell embryos

growth_protocol: E14tg2a mouse embryonic stem cells were grown on 0.1% gelatin in ES cell culture media; DMEM (1x) high glucose + glutamax (Gibco),  supplemented with 10% FCS (Greiner) 100 μM ß-mercaptoethanol (Sigma), 100 μM Non-essential amino acids (Gibco), 50 μg/mL Pen/Strep (Gibco)  and 1000 U/mL ESGRO mLIF (Millipore). Cells were split every 2 days and media changed every day.

extract_protocol:
Cells were harvested before sorting by washing 3 times with 1x PBS with calcium and magnesium and incubated with 0.05% trypsin (Life Technologies). Cell were resuspended in ES culture media and cell clumps were removed by passing the cells through a BD Falcon 5mL polystyrene tube with a filter top. One cell per well was sorted into 4titude Framestar® 384 well plates containing 4 μL VaporLock (Qiagen) and 0.2 μL lysis buffer. Doublets were removed by selecting for forward and side-scatter properties. Plates were centrifuged at 1000 rpm for 1 min directly post sorting to ensure that cells reach the aqueous phase. For embryo isolation, B6/CBA mouse oocytes were obtained from four 3 month old superovulated mothers (injected with pregnant mare serum gonadotropin (PMSG) and human chorionic gonadotropin (HCG) 22 hours later) and incubated in 10 mM SrCl2 (Sigma) for 2 hours in M16 medium to induce parthenogenic activation. Developing parthenogenic embryos were monitored hourly and sister cells were isolated using hyaluronic acid (Sigma) and trypsin (Life Technologies) post cytokinesis.
Robotic Preparation: 4 μL Vapor-Lock (Qiagen) is dispensed manually into each well of a 384 well plate using a multichannel pipet. 0.2 μL of lysis buffer (1x NEB buffer 4, 0.1 μg Qiagen protease) is dispensed at 12 psi pressure into each well using a Innovadyne NanoDrop II robot. Single cells are sorted into each well and the plate is incubated at 50°C for 3 hours, 75°C for 20 min and 80°C for 5 min. 0.2 μL of Glucosylation mix (1x NEB buffer 4, 2 U NEB T4-BGT, 1x NEB UDP-Glucose) is added and the plate is incubated at 37°C for 18 hours. Next, 0.2 μL of lysis buffer is added and the plate is incubated at 50°C for 3 hours, 75°C for 20 min and 80°C for 5 min. 0.2 μL of AbaSI (1x NEB buffer 4, 2 U NEB AbaSI) is added and the plate is incubated at 25°C for 1 hour and 65°C for 20 min. 0.2 μL of 0.01 μM adapter is added, followed by 0.2 μL of ligation mix (80 U T4-Ligase, 2X T4-ligase buffer, 0.6 mM ATP) and the plate is incubated for 16 hours at 16°C. Contents of all the wells with different adapters are pooled and incubated with 0.8x Agencourt Ampure XP beads for 30 min, washed twice with 80% ethanol and resuspended in 6.4 μL nuclease free water. 9.6 μL of in vitro transcription mix is added (1.6 μL of each ribonucleotide, 1.6 μL T7 buffer, 1.6 μL T7 enzyme mix) and incubated at 37°C for 14 hours. Thereafter, library preparation is performed as described in the CEL-Seq protocol with minor adjustments28. After in vitro transcription, the aRNA  (amplified RNA) is size selected by incubating with 0.8x Agencourt RNAClean beads for 30 min, washed twice with 70% ethanol and resuspended in 16 μL nuclease-free water. Next, the aRNA is fragmented using fragmentation buffer (200mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc) at 94°C for 1.5 min and quenched by putting the reaction on ice and adding 2 μL 0.5 M EDTA. Fragmented aRNA is then purified using 1x Agencourt RNAClean beads as mentioned before and eluted in 16 uL nuclease-free water. After these steps, library preparation is performed as described in the CEL-Seq protocol. Manual Preparation: Cells were transferred with a mouth pipette into 20 μL Vapor-Lock in the cap of a 0.5 mL tube. Thereafter, all steps are performed using 1 μL volumes (instead of 0.2 μL volumes used in the robotic preparation) with a P2 Gilson pipette. Samples are pooled, purified using 0.8x Agencourt Ampure XP beads and the library is prepared as described in the CEL-Seq protocol.
OTHER (scAba-seq). For details see: Mooijman et al. 2016 Nature Biotechnology

treatment_protocol: Vitamin C treatment of E14 cells: Vitamin C (L-ascorbic acid 2-phosphate, Sigma, A8960) was added to E14tg2a cells in a final concentration of 1 μg/mL 24 hours after splitting the cells. After 18 hours, the cells were washed three times with 1x PBS with calcium and magnesium and harvested using 0.05% trypsin (Life Technologies). Cell were resuspended in ES culture media and cell clumps were removed by passing the cells through a BD Falcon 5 mL polystyrene tube with a filter top.

value: Oocytes, 2-cell and 4-cell embryos


title: VitC E14 single cells - Library 1

source_name: Embryonic stem cells

value: Vitamin C


title: VitC E14 single cells - Library 2


title: Patient 15 Normal


title: E14 single cells - Library 4


title: E14 single cells - Library 3


title: E14 single cells - Library 2


title: Patient 13 Normal


title: E14 single cells - Library 1


title: Patient 12 Normal


title: Patient S Nasal 2

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: The Jenner Institute, University of Oxford

data_processing:
Illumina Casava v1.8 was used for basecalling.
Reads were adapter removed and trimmed to 70Bp using trimmomatic 0.32 with parameters ILLUMINACLIP:/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa:2:30:10 HEADCROP:15 CROP:70 SLIDINGWINDOW:6:5 MINLEN:70
Sequences were mapped to USA300_FPR3757 using bowtie2 v2.2.2 with parameters -N 0 --sensitive --fr -q --no-mixed --no-discordant  --no-unal
Genome_build: Staphylococcus aureus subsp. aureus USA300_FPR3757, assembly GCA_000013465.1
Supplementary_files_format_and_content: tab-delimited text files include per gene read counts. Counts were calculated using htseq-count from the HT-Seq package v0.6.1 with parameters: -f bam -r pos -s reverse -a 10 -t gene -i Name -m union

organism: Staphylococcus aureus

source_name: C24365_isolated from Patient S nasal tissue

growth_protocol: Staphylococcus aureus strains isolated from human samples were grown on Tryptic Soy agar (TSA), Trypticase soy broth supplemented with glucose (TSB + Glc) (0.25%, wt/vol), B2 medium (1% casein hydrolysate, 2.5% yeast extract, 2.5% NaCl, 0.1% K2HPO4, and 0.5% glucose [wt/vol]) with appropriate antibiotics wherever needed. Nasal swabs were plated on SASelect agar (BioRad) overnight at 37 ºC, and individual colonies were subcultured onto horse blood agar (Oxoid). Blood cultures used the BD Bactec system; media from the positive bottles was plated on horse blood agar, and colonies were picked from each bottle for sequencing. For RNA extraction, cultures of all samples listed above were prepared by picking 4 colonies from HBA to inocculate TSB and incubate overnight until stationary phase.

extract_protocol:
RNA was isolated using the RNeasy Protect Bacteria Kit (Qiagen) according to the manufacturer instructions (protocol 4). DNase I (DNAfree kit, Ambion) was used to remove remaining DNA. The concentration of the RNA was determined by spectrophotometry via fluorometry using the Qubit Fluorometer RNA BR Kit (Invitrogen). Quality and quantity of the RNA was examined by analysis on Tapestation (Agilent Technologies).
Sequencing libraries were constructed using the NEBNext Ultra Directional Library Preparation Kit for Illumina (#E7420 ,NEB)

tag: isolated from

value: Patient S

tag: tissue source

value: Nasal

tag: replicate


title: USA300 NE1304 2

source_name: USA300_in vitro culture

value: in vitro


title: Patient P Nasal 2

source_name: C11585_isolated from Patient P nasal tissue

value: Patient P


title: Patient 4 Normal


title: Patient P Blood 2

source_name: C1360_isolated from Patient P blood

value: Blood


title: Patient S Blood 1

source_name: C24366_isolated from Patient S blood


title: USA300 JE 2

value: USA300 JE2


title: Patient S Nasal 1


title: E14 single cells - Library 5

tag: cell type


title: Patient P Blood 1


title: E14 Bulk 5hmC


title: Patient S Blood 2


title: USA300 NE1304 1


title: USA300 JE 1


title: G6PD_NX-10

city: Rochester

first: Joseph

last: Miano

state: NY

address: 601 Elmwood Avenue, Box CVRI

department: Aab Cardiovascular Research Institute

institute: University of Rochster

data_processing:
Illumina bcltofastq v1.8.4 software used data formatting and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.4.2a with parameters --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Coronary arteriy (LAD)

extract_protocol:
TotalRNA was extracted from aortas using Qiagen miRNEasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cardiac

value: post natal week 12-16


title: CYPKO_NX-5_R

value: wild type


title: G6PD_NX-12


title: CYPKO_NX-6_R


title: Retina RNASeq Roxadustat 6

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Base calls performed using bcl2fastq version 1.8.3
RNA-Seq reads were aligned to the mouse reference genome (mm9) using Tophat version 2 with default parameters
Differential expression was determined using Cuffdiff version 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values given in a data matrix in tab delimited format (gene by sample).

extract_protocol:
RNeasy (Qiagen)
Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold

value: Roxadust

value: Retina


title: Retina RNASeq Roxadustat 5


title: Retina RNASeq Roxadustat 4


title: CYPKO_NX-4_R


title: Retina RNASeq Roxadustat 2


title: Retina RNASeq Roxadustat 1


title: Patient P Nasal 1


title: Retina RNASeq DMOG 5

value: DMOG


title: Retina RNASeq DMOG 3


title: Retina RNASeq DMOG 2


title: Retina RNASeq DMOG 4


title: Retina RNASeq DMOG 1


title: Kat2b-Chip-seq_1

city: Lille

first: Jean Sébastien

last: Annicotte

address: Faculté de Médecine - Pôle recherche 2ème étage 1 place de Verdun

country: France

institute: CNRS UMR8199

data_processing:
Basecalls performed using CASAVA version1.8.2
sequences were Trimmed using Trim sequences  Version 1.0.0 (First base to keep 9 and Last base to keep 50)
Remove PCR duplicates using rmdup Version 1.0.0
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 1.1.1 with default configurations
Datasets were concatenate  tail-to-head
peaks were called using MACS version  1.0.1 with the following setting: Pvalue cutoff for peak detection 0.00001
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS version 1.0.1

source_name: isolated mouse islet

extract_protocol:
ChIP assays were performed in triplicates on approximately 600 mouse isolated islets using True MicroChIP kit (Diagenode) following manufacturer’s protocol. .
ChIP-seq libraries were prepared using NEBNext-Ultra kits (New England Biolabs) following manufacturer’s instructions. DNA libraries were quantified by Qubit (Invitrogen) and were sequenced using a Hiseq 2500 instrument in single end 50pb reads (illumina).

value: adult 10-12 weeks old

tag: antibody

value: Kat2b (Abcam; ab12188)


title: Kat2b-Chip-seq_3


title: Kat2b-Chip-seq_2


title: G6PD_NX-11


title: Input for Kat2b


title: Retina RNASeq DMOG 6


title: Retina RNASeq PBS 6

value: PBS


title: Retina RNASeq PBS 4


title: Retina RNASeq PBS 5


title: Retina RNASeq PBS 3


title: Retina RNASeq PBS 2


title: Retina RNASeq PBS 1


title: Liver RNASeq Roxadustat 6

value: Liver


title: Liver RNASeq Roxadustat 4


title: Liver RNASeq Roxadustat 5


title: Retina RNASeq Roxadustat 3


title: Liver RNASeq Roxadustat 2


title: Liver RNASeq Roxadustat 3


title: Liver RNASeq Roxadustat 1


title: Liver RNASeq DMOG 6


title: PreImmune_ChIPSeq

city: Zaragoza

first: Jon

last: Schoorlemmer

address: c/Juan Bosco 13, planta A

department: Retroviral elements in development and disease

country: Spain

institute: ARAID

data_processing:
Basecalls performed using CASAVA version 1.7.0
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9, maximum 1 mismatch
Data were filtered using the following specifications: we differentiate reads mapping at several positions on the genome (non-unique or R) from reads mapping at a unique position (U) (based on Phred scores)
Peaks were called using Seqmonk version V0.16.0  with the following setting: no threshold for two different datasets: R and U.
Peaks were loaded into excel, counts of 0 were substituted for 1. Counts in the YY2 dataset were multiplied by 1.62 to normalize for the number of mm9-mapped reads in each dataset. An arbitrary score was calculated for each peak as the number of normalized reads in αYY2 IP divided by the number of reads in the PreI sample in the same window (separated scores for unique and non-unique =R reads).
Genome_build: mm9
Supplementary_files_format_and_content: The Seqmonk output is in .tsv files for YY2 (GEY10.tsv) and Preimmune serum (GEY11.tsv), respectively. An Excel book (YY2_TS list) is provided with several sheets that list the peaks from high to low scores based on either (non-unique = R) or (unique = U) reads, respectively. Scores in the R+U file represent values calculated as the product of the enrichment values obtained for R and U separately.

source_name: Trophectoderm Stem cells

growth_protocol: TSB7 TS cells were routinely maintained in MEF-conditioned medium supplemented with 25 ng/ml of FGF-4 as described (Mak W et al., (2002) Curr Biol.12(12):1016-20).

extract_protocol:
ChIPseq protocol from Pérez-Palacios et al., 2016. 5 x 106 cells for each experimental condition were chemically crosslinked for 15 min at room temperature by the addition of fresh 37% formaldehyde solution to a final concentration of 1% (v/v). After the addition of glycine to a final concentration of 125 mM to stop the crosslink, cells were rinsed twice with PBS and harvested by scraping. Cells were resuspended in lysis buffer (50mM Tris-HCl (pH 8.1), 10mM EDTA, 1% (w/v) SDS) and protease inhibitors (CompleteTM, Roche) and sonicated in a Diagenode sonicator (30 second pulses, 30 second pause between pulses).
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols using a TruSeq (TM) SBSv5 sequencing kit..
ChIP-Seq, instrument version Illumina Hi-Seq 2000, sequencing cycles 50

value: Trophoblast precursors

tag: antibodies

value: Described in Garcia-Tuñon I et al. Stem Cell Res.(2011)7(1), 1-16. and in Pérez-Palacios et al., 2016.

value: Mak et al., 2012


title: YY2_ChIPSeq

tag: passages

value: 12 after receipt

value: In house aYY2 polyclonal rabbit serum

value: (C57B16xCBA)F1 females and PGK strain males


title: Liver RNASeq DMOG 5


title: Liver RNASeq DMOG 3


title: Liver RNASeq DMOG 4


title: Liver RNASeq DMOG 2


title: Liver RNASeq PBS 5


title: M24Col

city: Seattle

first: Julia

last: Cui

state: Washington

address: 4225 Roosevelt Way NE Suite # 100

institute: University of Washington

data_processing:
bcl files converted to qseq and fastq files using the Illumina Casava software
Quality control using Fastqc, all reads kept
fastq files mapped to mm10 using Tophat-2.0.3 (bowtie-0.12.8)
SAM to BAM conversion and sorting: samtools-0.1.18
mRNA abundance etimation using Cufflinks-2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, FPKM

source_name: Large intestine

extract_protocol:
Livers were collected after removing the gallbladder. Intestinal contents were flushed with phosphate buffered saline and intestinal tissues were separated into various sections, namely duodenum, jejunum, ileum, and large intestine (colon).  All tissues were snap-frozen in liquid nitrogen and stored at -80˚C.Total RNA was isolated from tissues using RNA Bee reagent and RNA integrity was confirmed using a dual Agilent 2100 Bioanalyzer (RIN>7.0).
The cDNA libraries from total RNA samples were prepared using an Illumina TruSeq RNA sample prep kit. Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer’s protocol.

value: Large intestine

value: 2-3 months

tag: Sex

value: male


title: Liver RNASeq PBS 6

tag: tissue


title: Liver RNASeq PBS 4

tag: strain


title: Liver RNASeq DMOG 1


title: M27Col

tag: age

value: wild type


title: Liver RNASeq PBS 3

tag: treatment


title: M24Ile

source_name: Ileum

value: Ileum


title: M25Ile


title: Liver RNASeq PBS 2


title: M27Ile


title: M25Col


title: M28Jej

source_name: Jejunum

value: Jejunum


title: M24Jej


title: M27Duo

source_name: Duodenum

value: Duodenum


title: AMPK R299Q Knock-in Homozygote 7

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description:
total RNA extracted from the hypothalamic arcuate nucleus from homozygous AMPK R299Q knock-in mice
Hom7

data_processing:
Reads were aligned to the GRCm38/Ensembl V54 transcriptome using Tophat v2.0.8 with default parameters
Counts and differential gene expression were determined using CuffLinks v2.2.1 using default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM values in tab-delimited txt format

source_name: Hypothalamic Arcuate Nucleus

growth_protocol: Ad Libitum Fed

extract_protocol:
The hypothalamic arcuate nucleus was extracted from 14um brain cryosections using laser capture microdissection.  RNA was extracted usiing Qiagen RNeasy Plus Micro kit.
RNA was subjected to whole-transcriptome amplification using NuGEN RNAseq v2 System to make dsCDNA, this was followed by fragmentation to 200bp with a Diagenode Bioruptor Pico sonicator. The resulting fragments were then used to make bar-coded libraries using NuGEN Ovation Rapid DR Multiplex System

value: Homozygous AMPK R299Q

value: brain


title: M28Duo


title: AMPK R299Q Knock-in Homozygote 6

description:
total RNA extracted from the hypothalamic arcuate nucleus from homozygous AMPK R299Q knock-in mice
Hom6


title: Liver RNASeq PBS 1

value: PBS


title: M24Duo


title: Homozygous AMPK R299Q Knock-in  5

description:
total RNA extracted from the hypothalamic arcuate nucleus from homozygous AMPK R299Q knock-in mice
Hom5


title: M27Liv

source_name: Liver

value: Liver


title: M26Liv


title: M24Liv


title: Homozygous AMPK R299Q Knock-in  4

description:
total RNA extracted from the hypothalamic arcuate nucleus from homozygous AMPK R299Q knock-in mice
Hom4


title: M27Jej


title: Homozygous AMPK R299Q Knock-in  3

description:
total RNA extracted from the hypothalamic arcuate nucleus from homozygous AMPK R299Q knock-in mice
Hom3


title: Homozygous AMPK R299Q Knock-in  2

description:
total RNA extracted from the hypothalamic arcuate nucleus from homozygous AMPK R299Q knock-in mice
Hom2


title: Homozygous AMPK R299Q Knock-in  1

description:
total RNA extracted from the hypothalamic arcuate nucleus from homozygous AMPK R299Q knock-in mice
Hom1


title: Cytoplasmic_1

city: St Louis

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
Single-end 100 bp read ends trimmed using Trimmomatic
Samples mapped to rRNA sequences using Bowtie2
Excluded two samples
Surviving reads mapped to Ensembl v. 75 of genome using STAR
Counting reads performed using BedTools
Removed genes with biotype other than protein_coding, lincRNA, sense_overlapping snoRNA, or snRNA
Differential expression analysis performed using EdgeR
Read counts fit to negative binomial generalized log-linear model
Likelihood ratio test done to determine differential expression
Multiple correction testing done using Benjamini-Hochberg's false discovery rate algorithm
Genome_build: Ensembl 75 (mouse)
Supplementary_files_format_and_content: CSV file with counts for each gene (rows) and sample (columns)

source_name: Mouse Brain Cytoplasm_Cytoplasmic

extract_protocol:
Trizol, DNAse Treatment, Qiagen RNAeasy minelute
Nugene Ovation RNAseq V2

tag: mouse line

value: 6-12 Weeks

value: M

value: whole Brain

value: Astrocyte

tag: molecule subtype

value: cytoplasmic RNA


title: Wild-type 5

description:
total RNA extracted from the hypothalamic arcuate nucleus from wild type mice
WT5

tag: genotype/variation

value: Wild Type


title: 920_Sorted_M_Neuro_2

source_name: Mouse Brain Nuclei_Sorted_M_Neuro

value: Neuron

value: nuclear RNA


title: 920_Sorted_M_Astro_8

source_name: Mouse Brain Nuclei_Sorted_M_Astro


title: Wild-type 2

description:
total RNA extracted from the hypothalamic arcuate nucleus from wild type mice
WT2


title: 920_Sorted_M_Neuro_4


title: Wild-type 4

description:
total RNA extracted from the hypothalamic arcuate nucleus from wild type mice
WT4


title: Cytoplasmic_2

value: F

value: Oligodendrocyte


title: 920_Sorted_F_Oligo_36

source_name: Mouse Brain Nuclei_Sorted_F_Oligo


title: 920_Sorted_F_Neuro_28

source_name: Mouse Brain Nuclei_Sorted_F_Neuro


title: 920_Sorted_M_Astro_6


title: 920_Sorted_M_Oligo_10

source_name: Mouse Brain Nuclei_Sorted_M_Oligo


title: KD3

data_processing:
Following generation of sequencing images, the pixel-level raw darta collection, image analysis, and base-calling were performed by Real Time Analysis software (Illumina)
Base call files were converted to qseq files by BCL converter (Illumina), and qseq files were converted to fastq files for downstream analysis.
Reads from fastq files were mapped to the rat reference genome (Rnor_5.0.7) using CLC Bio Genomics Workbench 7.0 (CLC Bio, Aarhus, Denmark)
Genome_build: Rnor_5.0 [Rnor_5.0.7 (Rat)]
Supplementary_files_format_and_content: excel file containing reads per kilobase per million reads (RPKM).

source_name: Rcho1 cells

growth_protocol: Rcho-1 TS cells were maintained in Stem State Medium [RPMI-1640 culture medium (Gibco-Life Technologies, Carlsbad, CA) supplemented with 20% fetal bovine serum (FBS: Atlanta Biologicals, Norcross, GA), 50 μM 2-mercaptoethanol (Sigma-Aldrich, St Lois, MO), 1 mM sodium pyruvate, 100 μM penicillin, and 100 U/ml streptomycin], as previously reported (Faria and Soares 1991; Sahgal et al. 2006).  Rcho-1 TS cells were grown to near confluence and differentiation was induced by replacing the Stem State Medium with Differentiation State Medium [NCTC-135 medium (Sigma-Aldrich) supplemented with 1% horse serum (HS; Atlanta Biologicals), 50 μM 2-mercaptoethanol, 1 mM sodium pyruvate, 10 mM HEPES, 4-(2-hydroxyethy)-1-piperazineethanesulfonic acid, 38 mM sodium bicarbonate, 100 μM penicillin and 100 U/ml streptomycin.

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's recommendations.
Libraries were prepared from poly-A containing RNAs according to protocols provided by the TruSeq RNA sample preparation kits (Illumina). 500 ng of RNA from cells expressing control shRNA (3 replicates) or Cited2 shRNA (3 replicates) was used as input.

treatment_protocol: Cells were transduced via lentivirus with control shRNA or an shRNA targeting Cited2.

value: Lewis (LEW/SsNHsd)

tag: gender

value: female

value: 4 weeks

tag: cell line

value: Cited2 shRNA

tag: sampling interval post tretament

value: 8 days differentiation


title: 920_Sorted_F_Neuro_26


title: 920_Sorted_F_Astro_32

source_name: Mouse Brain Nuclei_Sorted_F_Astro


title: 920_Sorted_M_Oligo_12


title: 920_Presort_M_Oligo_9

source_name: Mouse Brain Nuclei_Presort_M_Oligo

value: Mixed


title: Wild-type 1

description:
total RNA extracted from the hypothalamic arcuate nucleus from wild type mice
WT1

value: brain


title: Wild-type 3

description:
total RNA extracted from the hypothalamic arcuate nucleus from wild type mice
WT3


title: Control 3

value: Control shRNA


title: 920_Presort_M_Oligo_11

value: 6-12 Weeks

value: M


title: 920_Presort_M_Neuro_3

source_name: Mouse Brain Nuclei_Presort_M_Neuro

value: whole Brain


title: KD2


title: 920_Sorted_F_Astro_30

value: Astrocyte


title: Control 1


title: 920_Presort_M_Neuro_1


title: 920_Sorted_F_Oligo_34


title: 920_Presort_M_Astro_7

source_name: Mouse Brain Nuclei_Presort_M_Astro


title: rgef-1p::jmjd-1.2 EV replicate 3

city: Berkeley

first: Andrew

last: Dillin

state: CA

address: 188 Li Ka Shing

institute: University of California, Berkeley

data_processing:
Illumina HiSeq 2500 reads were trimmed of adapter sequences and filtered for read that passed quality filtering
Reads were mapped to a set of C. elegans noncoding RNAs
Remaining reads were mapped to an index containing the longest single isoform ± 30nt for each gene in the C. elegans WS230 genome using Bowtie version 0.12.7 (Langmead et al., 2009) with the following settings: -m 1 -v 2 -a --norc --best --strata
In-house python scripts were used to count reads mapping to each transcript.
Tab-delimited .txt files include raw counts associated with each transcript and can be used as input for DESeq, where we used a standard pipeline to determine differential expression by padj < 0.05
Genome_build: WS230
Supplementary_files_format_and_content: Tab-delimited .txt files include raw counts associated with each transcript

organism: Caenorhabditis elegans

source_name: whole worm lysate

growth_protocol: Animals were grown from hatch at 20C on empty vector bacteria.

extract_protocol:
Collected worms were snap frozen in liquid nitrogen. Pellets were grinded with a mortar and pestle on dry ice and the resulting powder was thawed in the presence of lysis buffer (50mM Tris-HCl, 50mM NaCl, 10mM MgCl2, 5mM CaCl2 200μg/ml cycloheximide, 200μg/ml heparin, 1% Triton X-100, 0.1% NaDOC) and incubated on ice for 10 minutes prior to centrifugation at 4C, 16,000 x g for 10 minutes.  Total RNA was purified from clarified lysate using Trizol-LS (Life Technologies) and poly-A RNA was extracted with oligo-dT(25) Dynabeads (Ambion), each according to manufacturer’s instructions.
Sequencing libraries were prepared using the Epicentre ScriptSeq v2 according to manufacturer’s instructions.

treatment_protocol: Animals were collected by washing with M9 at the L4 stage.

tag: strain/line background

tag: developmental stage

tag: RNAi treatment

value: empty vector (EV)

value: whole worm lysate


title: KD1


title: rgef-1p::jmjd-1.2 EV replicate 2


title: 920_Presort_M_Astro_5

tag: cell type

value: nuclear RNA


title: rgef-1p::jmjd-1.2 EV replicate 1


title: jmjd-3.1::jmjd-3.1 EV replicate 3

value: cco-1 + empty vector (EV)


title: 920_Presort_F_Oligo_33

source_name: Mouse Brain Nuclei_Presort_F_Oligo

value: F


title: 920_Presort_F_Neuro_25

source_name: Mouse Brain Nuclei_Presort_F_Neuro


title: Control 2

value: Lewis (LEW/SsNHsd)


title: 920_Presort_F_Oligo_35


title: 920_Presort_F_Neuro_27


title: jmjd-3.1::jmjd-3.1 EV replicate 2


title: N2 cco-1 replicate 2


title: N2 cco-1 replicate 1


title: N2 EV replicate 3


title: jmjd-3.1::jmjd-3.1 EV replicate 1


title: N2 cco-1 replicate 3


title: N2 EV replicate 1


title: met-2(ok2307) cco-1 replicate 2

data_processing:
Illumina HiSeq 2500 reads were trimmed of adapter sequences and filtered for read that passed quality filtering
Reads were mapped to a set of C. elegans noncoding RNAs
Remaining reads were mapped to an index containing the longest single isoform ± 30nt for each gene in the C. elegans WS230 genome using Bowtie version 0.12.7 (Langmead et al., 2009) with the following settings: -m 1 -v 2 -a --norc --best --strata
In-house python scripts were used to count reads mapping to each transcript.
Tab-delimited .txt files include raw counts associated with each transcript and can be used as input for DESeq, where we used a standard pipeline to determine differential expression by padj < 0.05
Genome_build: Wormbase WS230
Supplementary_files_format_and_content: Tab-delimited .txt files include raw counts associated with each transcript

source_name: met-2(ok2307) cco-1_whole worm lysate

growth_protocol: N2, lin-65(n3441) and met-2(ok2307) animals were grown from hatch at 20C on either empty vector (EV) or EV+cco-1 RNAi bacteria.


title: sur-5p::jmjd-1.2 EV replicate 3


title: sur-5p::jmjd-1.2 EV replicate 1


title: met-2(ok2307) EV replicate 3

source_name: met-2(ok2307) EV_whole worm lysate


title: sur-5p::jmjd-1.2 EV replicate 2


title: met-2(ok2307) EV replicate 2


title: 920_Presort_F_Astro_31

source_name: Mouse Brain Nuclei_Presort_F_Astro


title: met-2(ok2307) EV replicate 1


title: lin-65(n3441) cco-1 replicate 3

source_name: lin-65(n3441) cco-1_whole worm lysate


title: met-2(ok2307) cco-1 replicate 1


title: lin-65(n3441) cco-1 replicate 1


title: lin-65(n3441) cco-1 replicate 2


title: N2 EV replicate 3

source_name: N2 EV_whole worm lysate


title: N2 EV replicate 2


title: lin-65(n3441) EV replicate 2

source_name: lin-65(n3441) EV_whole worm lysate


title: N2 cco-1 replicate  1

source_name: N2 cco-1_whole worm lysate


title: N2 cco-1 replicate 2


title: met-2(ok2307) cco-1 replicate 3


title: lin-65(n3441) EV replicate 3


title: N2 cco-1 replicate 3


title: N2 EV replicate 1


title: N2 EV replicate 2


title: MD231

first: Stephen

last: Lindemann

address: 745 Agriculture Mall Drive

department: Food Sciences

data_processing:
Measurement of gene expression was performed in seven RNA-Seq experiments using a Life Technologies SOLiD 3 sequencer. The short read sequences produced by the SOLiD 3 sequencer were mapped in color space using the Life Technologies BioScope software version 1.3. (https://abcommunity.thermofisher.com/groups/solid-news/blog/2010/11/10/solid-bioscope-software-13-now-available).  The default settings were used in the Life Technologies BioScope software. Precise BioScope version: bioscope-v1.3-rBS131_55029_20101119113500. The reference genome was the human genome UCSC hg19, released Feb 2009. (See https://genome.ucsc.edu/FAQ/FAQreleases.html)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited gene rollup text files listing the gene counts for each sample

source_name: Cell culture

growth_protocol: All breast cell lines were obtained from the ATCC and grown as described (PMC3845839). Cells were plated in 15 cm dishes or 96 well plates, grown for 24 hours, starved in serum-free media for 18h, and starved again for an additional hour prior to treatment. NHDF cells (primary neonatal fibroblasts) were obtained from Lonza and cultivated according to manufactors instructions.

extract_protocol:
Cells were washed 2x with ice cold PBS, lysed in 1ml of RLT buffer (RNeasy Mini Kit, Qiagen) supplemented with 1:100 β-mercaptoethanol, transferred to a micro-centrifuge tube, and snap-frozen in liquid nitrogen.
Genomic DNA was removed from RNA samples using a Qiagen RNase-Free DNase Set kit. RNA integrity was ascertained with a Bioanalyzer and all samples had an RNA integrity number (RIN) between 9 or 10. Ribo-zero Gold rRNA removal kit was used to enrich transcripts and a SOLiD® Total RNA-Seq Kit was used to construct template cDNA for RNA-Seq. The ribosomal depleted mRNA was fragmented using hydrolysis, followed by ligation with strand specific adapters and reverse transcript to generate cDNA. Fragments > 150 bp were subsequently selected using Agencourt Ampure XP beads. The isolated cDNA went through 15 cycles of amplification to produce enough templates for the SOLiD™ EZ Bead™ system to generate a templated bead library for ligation-based sequencing on the 5500XL SOLiD™ platform using barcoding, with a minimum of 2.2 x 107 mapped reads per cell line.

treatment_protocol: No experimental treatments

value: Breast carcinoma

tag: cell number per plate


title: MCF7


title: NHDF

value: Primary neonatal fibroblasts

value: NHDF-Neo


title: E11.5_head tech rep

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

institute: IGMM MRC Human Genetics Unit

data_processing:
The sequencing data was processed through a Torrent 5C data transformation pipeline on Galaxy (https://main.g2.bx.psu.edu/). The data was mapped against a customized reference file with TMAP. The reference file contained a list of all possible contacts between Forward and Reverse 5C primers covering our regions.
The data was then filtered to remove low-quality reads (MAQ quality score of lower than 30), reads aligning more than two nucleotides away from the reference sequence start site, and reads which do not contain EcoRI restriction sites.
5C data was normalized by dividing the number of reads of each 5C contact by the total number of reads from the corresponding sequence run multiplied by 10^3.
Genome_build: mm9
Supplementary_files_format_and_content: This analysis generates a matrix file containing the interaction frequencies.  The .tab files column header names are: region, primer name, assembly, chromosome, start position, end position, region, primer name, assembly, chromosome, start position, end position, genomic distance, 5C count.

source_name: Embryonic heads

extract_protocol:
10-20 million fixed cells were incubated for 15 min on ice in 200 ml of lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP40, supplemented with fresh protease inhibitor cocktail).  Cells were then disrupted on ice with a dounce homogenizer (pestle B; 2 x 20 strokes), cell suspensions transferred to eppendorf tubes and centrifuged 5 min at 2000 g.  Supernatants were removed, the cell pellets washed twice with 100 ml of 1X CutSmart buffer (NEB) and the cell pellet resuspended in 100 ml of 1X CutSmart buffer, and divided into two eppendorf tubes.  1X CutSmart buffer (337 ml) was added to each tube, and the mixture was incubated 10 min at 65°C with 0.1% SDS.  44 ml of 10% Triton X-100 were added before overnight digestion with 400 Units HindIII.  The restriction enzyme was then inactivated by adding 86 ml of 10% SDS, and incubation for 30 min at 65°C.  Samples were then individually diluted into 7.62 ml of ligation mix (750 ml 10% Triton X-100, 750 ml 10X ligation buffer, 80 ml 10 mg/ml of BSA, 80 ml 100 mM ATP and 3000 Cohesive end Units of T4 DNA ligase) and incubated at 16°C for 2 hours. 3C libraries were incubated overnight at 65°C with 50 ml Proteinase K (10 mg/ml), and with an additional 50 ml Proteinase K the following day for 2 hours.  The DNA was purified by one phenol and one phenol-chloroform extraction, and precipitated with 0.1 volume (800 ml) of 3 M NaOAc pH 5.2 and 2.5 volumes of cold EtOH (20 ml).  After at least 1 h at -80°C, the DNA was centrifuged for 25 min at 20,000 g at 4°C, and the pellets washed with cold 70% EtOH. DNA was resuspended in 400 ml of TE pH 8.0, and transferred to eppendorf tubes for another phenol-chloroform extraction and precipitation with 40 ml of 3 M NaOAc pH 5.2 and 1.1 ml of cold EtOH.  DNA was recovered by centrifugation, and washed eight times with cold 70% EtOH.  Pellets were then dissolved in 100 ml TE pH 8.0, and incubated with RNAse A (1 ml at 10 mg/ml) for 15 min at 37°C.
3C libraries were denatured and annealed to 5C primers. 5C oligonucleotide were designed upstream (FORWARD) or downstream (REVERSE) EcoRI restriction sites. Annealing was followed by ligation with Taq DNA ligase. Ligated 5C primers were then amplified with the A-key and P1-key primers to generate the 5C libraries. 5C libraries were then prepared for sequencing onto Ion 316™ Chips with an Ion PGM™ Sequencer following either the Ion Xpress™ Template Kit v2.0, and Ion Sequencing Kit v2.0 protocols, or the Ion PGM™ Template OT2 200 Kit, and Ion PGM™ Sequencing 200 Kit v2.0 protocols as recommended by the manufacturer’s instructions (Life TechnologiesTM). Libraries were prepared according to Ion Torrent's instructions

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped with glycine (125 mM final concentration), and incubated for 5 min at room temperature followed by 15 min on ice. Cells were centrifuged at 400 g for 10 min at 4°C. Supernatants were removed and cell pellets were flash frozen on dry ice.

value: Embryonic neural, cranio-facial


title: MCF10A

value: Breast epithelial

value: MCF 10A


title: E11.5_body

source_name: Embryonic bodies

value: Embryonic multiple


title: HMEC

value: Immortalized non-tumorgenic breast epithelial


title: lin-65(n3441) EV replicate 1


title: BT20


title: E11.5_limb

source_name: Embryonic limb buds

value: Embryonic limb


title: Nutlin+Wip1i_rep1

status: Public on May 02 2016

city: Göttingen

first: Anusha

last: Sriraman

address: Justus-von-liebig Weg 11

department: Department of Molecular Oncology

country: Germany

institute: Georg-August University of Göttingen

data_processing:
demultiplexed to fastq files with CASAVA (version 1.8.2)
mapped to the mouse reference transcriptome (UCSC hg19) using TopHat (Galaxy Version 0.9)
Read counts for each sample and each gene were aggregated using a htseq-count
DESeq2 (version 1.10.1) was used for measuring differential expression
Genome_build: hg19
Supplementary_files_format_and_content: CSV files include RPKM values for each Sample

source_name: human breast adenocarcinoma cell line

growth_protocol: Cells were cultured in DMEM (Gibco/Life Technologies) supplemented with 10 % fetal calf serum (FCS) and antibiotics

extract_protocol:
Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies).
For RNA-sequencing, the quality of total RNA was determined using the bioanalyzer 2100 from Agilent. All samples analyzed exhibited a RIN>8. Library preparation was conducted using the TruSeq RNA LT SamplePrep Kit (Illumina) starting from 1000 ng of total RNA. Barcodes used for sample preparation were used according to the indications given by the protocol. Accurate library quantitation of cDNA libraries was performed with the QuantiFluor™dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (290-310 bp). cDNA libraries were amplified and sequenced via cBot and HiSeq 2000 from Illumina (SR, 1×50 bp, 6 Gb/sample ca. 30 million reads per sample). Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA (version 1.8.2).

tag: tissue type

value: breast adenocarcinoma


title: Nutlin+Wip1i_rep3


title: Wip1i_rep2


title: Wip1i_rep3


title: Synthetic 5hmC Spike-in

organism: synthetic construct

source_name: In vitro synthesized DNA molecules

tag: spike-in

value: Synthetic 5hmC Spike-in


title: E11.5_head

tag: tissue


title: Wip1i_rep1


title: SKBR3


title: Nutlin_rep3

value: Nutlin


title: DMSO_rep2

value: DMSO


title: DMSO_rep3


title: Nutlin_rep1


title: Nutlin_rep2


title: DMSO_rep1


title: H3K27me3 in Col-0 IP Replicate2

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
The reads were mapped onto the TAIR10 genome build using Bowtie
To identify regions that were significantly enriched, we used MACS and SICER with parameters of W:200 (Window length), G:600 (Gap size) for  for H3K27me3 and FDR <1E-2. Enriched regions were detected against the islands of background control with the same parameter.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using MACS

source_name: Arabidopsis thaliana Col-0

growth_protocol: Plants were grown in chambers at 20°C on sterile half-strength MS medium and 0.8% agar under long-days (16h of light at 20°C, 8h of darkness at 18°C).

extract_protocol: ChIP-seq assays were performed on 14-day-old in vitro shoot seedlings using anti-GFP (Clontech 632592), anti-H3K27me3 (Millipore 07-449).

treatment_protocol: Seeds were surface-sterilized by treatment with bayrochlore for 20 min, washed, and imbibed in sterile-water for 2–4 days at 4 °C to obtain homogeneous germination.

tag: ecotype

value: wild type

value: seeds

tag: chip antibody

value: anti-H3K27me3 (Millipore 07-449)


title: H3K27me3 in Col-0 Input Replicate2


title: H3K27me3 in lhp1 Input Replicate2

source_name: Arabidopsis thaliana lhp1 mutant

value: lhp1 mutant


title: RNAPol-II

value: wildtype

value: anti-RNA Pol II (Abcam ab817)


title: Nutlin+Wip1i_rep2

tag: treatment


title: H3K27me3 in CLF Input Replicate2

source_name: Arabidopsis thaliana clf mutant

value: clf mutant


title: H3K27me3 in CLF


title: LHP1 ChIPseq Input


title: H3K27me3 in WT, 1


title: LHP1 ChIPseq


title: E11.5_limb rep

data_processing:
The sequencing data was processed through a Torrent 5C data transformation pipeline on Galaxy (https://main.g2.bx.psu.edu/). The data was mapped against a customized reference file with TMAP. The reference file contained a list of all possible contacts between Forward and Reverse 5C primers covering our regions.
The data was then filtered to remove low-quality reads (MAQ quality score of lower than 30), reads aligning more than two nucleotides away from the reference sequence start site, and reads which do not contain EcoRI restriction sites.
5C data was normalized by dividing the number of reads of each 5C contact by the total number of reads from the corresponding sequence run multiplied by 10^3.
Genome_build: mm9
Supplementary_files_format_and_content: This analysis generates a matrix file containing the interaction frequencies.  The .tab files column header names are: region, primer name, assembly, chromosome, start position, end position, region, primer name, assembly, chromosome, start position, end position, genomic distance, 5C count..  The .tab files column header names are: region, primer name, assembly, chromosome, start position, end position, region, primer name, assembly,

tag: strain

tag: age


title: H3K27me3 in WT, 2

tag: genotype/variation


title: H3K27me3 in LHP1


title: Affected

status: Public on May 01 2016

city: Iowa City

first: S. Scott

last: Whitmore

state: IA

address: 375 Newton Road

department: The University of Iowa Institute for Vision Research

institute: The University of Iowa

description: RNA from cells of the iridiocorneal angle (tissue between the iris and the cornea)

data_processing:
Reads were mapped to the felCat5 genome build using Tophat (ver. 2.0.9) (--max-insertion-length 4, --read-mismatches 2, --read-gap-length 4, --read-edit-dist 4, -G with Ensembl gene predictions).
Transcript abundance and differential expression were calculated using the software Cufflinks  (ver. 2.1.1; http://cufflinks.cbcb.umd.edu/) and cummeRbund (ver. 2.4.1; http://compbio.mit.edu/cummeRbund/). Analysis parameters for Cufflinks were (--max-bundle-frags 20000000).
Genome_build: felCat5
Supplementary_files_format_and_content: tab-delimited text file of FPKM values for each locus detected by Cufflinks

organism: Felis catus

source_name: Iridiocorneal angle

extract_protocol:
Qiagen RNeasy (Qiagen, Valencia, CA)
Illumina TruSeq RNA sample preparation v2 kit (Illumina, Inc., San Diego, CA) with 500 ng input RNA following Illumina's protocol.

value: Iridiocorneal angle

tag: disease state

value: primary congenital glaucoma


title: Normal

value: normal


title: WRN_ChIP_Control

city: Philadelphia

first: Sager

middle: Jayesh

last: Gosai

state: Pennsylvania

address: 433 S University Ave.

department: Biology

institute: Universiry of Pennsylvania

data_processing:
Basecalls performed with Bustard 1.9.3.
3' adapter sequences were trimmed using cutadapt (version 1.2.1 with parameters -e 0.06 -O 6 -m 14)
Redundant reads were compressed using an in-house perl (version 5.8.8) script
Trimmed and untrimmed reads were aligned to the human genome (hg19) using Tophat (version 2.0.10 with parameters --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search –no-novel-juncs)
Peaks were called by using the WRN sequencing data as the experimental ChIP sample and the control sample as input in the MACS program using default parameters for sample versus input comparisons
Genome_build: hg19
Supplementary_files_format_and_content: BED format of ChIP-seq peaks called using the MACS software using the default settings.

growth_protocol: Human 293 embryonic kidney cells (from ATCC) were maintained in DMEM high glucose supplemented with 10% fetal bovine serum, penicillin (50 IU/mL), and streptomycin (50 µg/mL) at 37°C in atmosphere of 5% CO2.

extract_protocol:
Pellets were washed once again with PBS-PMSF, re-centrifuged 1800 x g 10 minutes at 4oC and resupended in cell lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, supplemented with Protease Inhibitor Cocktail Tablets (Roche Applied Science, Indianapolis, IN, USA)). After 10 minutes incubation on a rotating device at 4oC, lysates were homogenized using a dounce homogenizer (25 strokes) to facilitate nuclei release. Nuclei were pelleted 1800 x g 10 minutes at 4C and incubated in nuclei lysis buffer (50 mM trishydroxymethylaminomethane (Tris) pH 8, 10 mM EDTA, 1% sodium dodecyl sulfate (SDS), 1 mM PMSF and supplemented with Protease Inhibitor Cocktail Tablets (Roche Applied Science, Indianapolis, IN, USA)) for 10 minutes on ice. Nuclear extracts were sonicated with a Bioruptor (Diagenode, Liege, Belgium) in order to obtain chromatin fragment of approximately 500 bp. Samples were centrifuged for 30 minutes at 16,000 x g in a tabletop centrifuge at 4C. The supernatant was collected and diluted in 2 volumes of dilution buffer (0.1 % SDS, 1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8, 167 mM NaCl, 1 mM PMSF supplemented with Protease Inhibitor Cocktail Tablets (Roche Applied Science, Indianapolis, IN, USA)). Samples were subjected to pre-clearing with Dynabeads® Protein G (Invitrogen, Burlington, ON, Canada) for 2 h on rotating device at 4oC, and incubated with 10 mg of either anti-WRN or an IgG non specific to WRN protein (as control) overnight on a rotating device at 4C. The control IgG was a rabbit polyclonal antibody raised against Fatty Acids Synthase (H-300) purchased from Santa Cruz biotechnologies (Santa Cruz, CA, USA). Dynabeads® Protein G were then added to the mix for 4h. Samples were washed twice with dialysis buffer (2 mM EDTA, 50 mM Tris pH 8, 0.2% SDS) and four times with wash buffer (100 mM Tris pH 9, 0.5 M LiCl, 0.2% NP-40, 1% sodium desoxycholate). After the last wash, protein complexes were eluted from beads with elution buffer (1% SDS, 50 mM NaHCO3), heated for 10 minutes at 65C and mix on a vortex at medium speed for 15 minutes. Elution was performed twice and both supernatants were pooled. Cross-links were reversed overnight at 65°C in the presence of 0.2 M NaCl, and the samples were then treated with RNase A and proteinase K. DNA was purified with standard phenol/chloroform and ethanol precipitation procedures. Quantification of precipitated DNA fragment was performed by qPCR using PerfeCTa® SYBR® Green SuperMix®, Low ROX™ according to the manufacturer’s instructions.
ChIP DNA from the IgG control and WRN antibodies was used as the substrate for sequencing library preparation (TruSeq DNA sequencing kit [illumina, Valencia, CA]) per manufacturer instructions as previously described (Zheng et al. 2012).

treatment_protocol: A 20% PFA solution was added directly to the cell culture medium to obtain a final concentration of 1% PFA. The cells were incubated in the fixative for 10 minutes at room temperature. Quenching of excess PFA was performed by the addition of glycine 2.5 M solution to a final concentration of 125 mM. Cells were washed twice with ice-cold PBS containing 1 mM PMSF, scraped from the dish, harvested with the residual PBS and pelleted 1800 x g 10 minutes at 4oC.

tag: cell line

value: Human 293 embryonic kidney cells

tag: crosslinker

value: formaldehyde

tag: antibody used

value: IgG non specific antibody


title: WRN_ChIP

value: anti-WRN antibody


title: H3K27me3 in CLF IP Replicate2

tag: developmental stage


title: ND7/23

city: St Lucia

first: Kathleen

last: Yin

state: Queensland

address: 306 Carmody Rd

department: Institute of Molecular Biosciences

country: Australia

institute: University of Queensland

data_processing:
FASTQ data generation: CASAVA 1.8.2. Reads were screened for the presence of any adaptor or overrepresented sequences, ambiguous characters were clipped where required, and sequence bias was corrected.
Alignment: performed with Tophat with default analysis parameters in single-end mode. The number of mismatches were restricted to no more than 2 bases.
Assembly: Performed by Cufflinks with the reference annotation-based assembly option (RABT) using the UCSC annotation, and multi-reads correction was used.
Count: Gene counts were compiled using the HTSeq software
Genome_build: mm9 (DRGs, F-11, ND7/23), hg19 (SH-SY5Y), rn5 (F-11, ND7/23)
Supplementary_files_format_and_content: .txt files, tab-delimited.

organism:
Mus musculus
Rattus rattus

source_name: ND7/23 mouse neuroblastoma/rat DRG neuron

extract_protocol:
Whole DRGs were removed and immediately put into RNALater and cut into pieces in RNA later. RNA was extracted using the Rneasy Mini kit (Qiagen). Cultured cells were trypsinised and centrifuged and RNA was processed.
RNA libraries were prepared using for RNA-Seq

tag: genotype


title: F-11

source_name: F-11 mouse neuroblastoma/rat embryonic DRG neuron


title: 920_Presort_F_Astro_29

source_name: Mouse Brain Nuclei_Presort_F_Astro

tag: mouse line

value: 6-12 Weeks

tag: Sex

value: F

value: whole Brain

tag: cell type

value: Mixed

tag: molecule subtype

value: nuclear RNA


title: T4V RNA-seq replicate 1

city: Boston

first: Stirling

last: Churchman

state: MA

address: NRB Rm 356, 77 Ave Loius Pasteur

department: Genetics

institute: Harvard Medical School

description: total RNA was isolated by hot phoenol extraction and rRNA was depleted using Ribo-Zero Gold rRNA removel kit for yeast.

data_processing:
Libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice  (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net).
The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.
Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read.
For NET-seq only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python . For RNA-seq the same script was used this time recording the entire read.
RNAseq bedgraph files have been normalized by 10E4 unique RNA standard reads in the library.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: Chromosome, Start, End, Score

organism: Saccharomyces cerevisiae BY4741

source_name: yeast BY4741, mid-exponential phase

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
For NET-seq frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
For RNA-seq total RNA was extracted using standard hot phenol extraction from 2.34x10E8 cells and resuspeded in 30uL of RNase free water. 3uL A 1:10 dilution of ERCC RNA standards from Life Technologies was added to 5uL of total RNA.
For NET-seq a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads.
For RNA-seq total RNA after rRNA depletion was fragmented by alkaline hydrolysis followed by size selection after electrophoresis on a polyacrylamide gel.RNA was treated with polynucleotide kinase (NEB) followed by ligation to a preadenylated RNA linker. The remainder of the library construction was done as described inte NET-seq library construction. All samples were sequenced using an Illumina NextSeq 500 in 75 base pair reads

value: rpb3::rpb3-3xFLAG NAT, rpo21::rpo21-CTDT4V Kan


title: T4V RNA-seq replicate 2


title: WT RNA-seq replicate 2

value: rpb3::rpb3-3xFLAG NAT


title: H3K27me3 in lhp1 IP Replicate2

value: lhp1 mutant

value: seeds

value: anti-H3K27me3 (Millipore 07-449)


title: WT RNA-seq replicate 1


title: pSMF2_WTCTD1-8 NET-seq

description: nascent RNA isolated by IP against Rpb3-3x FLAG affinity label

data_processing:
Library strategy: NET-Seq
For NET-seq libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice  (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net). For ChIP-nexus reads were filtered for the presence of the fixed barcode CTGA, and for reads shorter than 60 basepairs the adapter sequence (AGATCGGAAGAGCACACGTCT) was trimmed.
For NET-seq the linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.For ChIP-nexus the remaining molecular barcode sequence was removed before alignment to the genome.
For NET-seq data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read. For ChIP-nexus data were aligned to the sacCer3 genome using Bowtie version 1.1.1 .
For both NET-seq and ChIP-nexus only the 5' position of the read is recorded with a custom python script using HTSeq package in python . NET-seq data are stranded while ChIP-nexus contain strand data merged into a single file that is unstranded.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: Chromosome, Start, End, Score

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8. For NET-seq in pSMF2 WT1-8 CTD and yKH303 T4V 1-8 CTD cells were grown at  30°C in sc-Lue media in the presense of 50 microgram per mL doxycylcine with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
For NET-seq frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004). For ChIP-nexus cells were crosslinked in 1% formaldehyde, lysed by bead beating, and sonicated. Chomatin was isolated via immunoprecipitation using phospoh-CTD antibodies or TAP tagged subunits.
For NET-seq nascent immunoprecipitated RNA was fragmented by alkaline hydrolysis followed by size selection after electrophoresis on a polyacrylamide gel.RNA was treated with polynucleotide kinase (NEB) followed by ligation to a preadenylated RNA linker. The remainder of the library construction was done as described inte NET-seq library construction. All samples were sequenced using an Illumina NextSeq 500 in 75 base pair reads. For ChIP-nexus the library constrution was preformed as desribed in He, Q., Johnston, J., Zeitlinger, J. (2015) "ChIP-nexus enables improved detection of in vivo transcription factor binding footprints." Nature Biotechnology. Samples were sequenced on an Illumina MiSeq in 60 bp single end reads.

value: Mat-alpha, his3delta, leu2delta, lys2delta, met15delta, trp1delta, hisG URA CMV-tTA, kanRPtetO7-TATA-RPB1 rpb3::rpb3-3xFLAG NAT pSMF2


title: T4V nascent RNA-seq

data_processing:
Libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice  (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net).
The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.
Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read.
For nascent RNA-seq the entire read is recorded with a custom python script using HTSeq package in python .
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: Chromosome, Start, End, Score

extract_protocol:
For nascent-seq frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
For nascent RNA-seq nascent immunoprecipitated RNA was fragmented by alkaline hydrolysis followed by size selection after electrophoresis on a polyacrylamide gel.RNA was treated with polynucleotide kinase (NEB) followed by ligation to a preadenylated RNA linker. The remainder of the library construction was done as described inte NET-seq library construction. All samples were sequenced using an Illumina NextSeq 500 in 75 base pair reads

value: BY4741, rpb3::rpb3-3xFLAG NAT, rpo21::rpo21-CTDT4V Kan


title: rtt103 delta NET-seq

description: nascent RNA isolated by IP agains Rpb3-3x FLAG affinity label

data_processing:
Library strategy: NET-Seq
Libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice  (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net).
The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.
Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read.
For NET-seq only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python . For RNA-seq the same script was used this time recording the entire read.
RNAseq bedgraph files have been normalized by 10E4 unique RNA standard reads in the library.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: Chromosome, Start, End, Score

value: BY4741, rpb3::rpb3-3xFLAG NAT, rtt103::HIS3


title: T4V NET-seq


title: rai1delta NET-seq

value: BY4741, rpb3::rpb3-3xFLAG NAT, rai1::HIS3


title: wild type NET-seq


title: wild type NET-seq replicate 2


title: wild type_endosperm

city: Shanghai

first: Weiwei

last: Qi

address: 333 Nanchen Road

institute: Shanghai University

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 B73 RefGen_v3 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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 fragments 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: Ensembl plants release-19 zea_mays/B73 RefGen_v3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: kernel

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: endosperm

value: 15 DAP

value: wild type


title: dek10 mutant_endosperm


title: wild type nascent RNA-seq

value: BY4741, rpb3::rpb3-3xFLAG NAT


title: cDC2 KO CRE+ 4

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: cDC2s from CD11cCRExZeb2fl/fl number 4

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

source_name: Spleen

growth_protocol: Spleens were harvested from mice aged between 6 and 12 weeks

extract_protocol:
Spleens were digested in RMPI containing 20mg/ML Liberase and 10U/ml DNase (37oC for 30minutes). Single cell suspensions were filtered through a 70mM strainer and stained with antibodies to allow cDC1s and cDC2s to be isolated by FACS.
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 4 ng of total RNA was used as input for the SMART-Seq v4 Ultra Low Input RNA protocol (version “040215”) from Clontech Laboratories, Inc. Subsequently, 1ng of purified cDNA was sheared to 300bp using the Covaris M220. From the sheared material, sequencing libraries were prepared with the NEBNext Ultra DNA Library Prep Kit for Illumina (version 3.0 -8/15), according to the manufacturer’s protocol including a size selection to 250bp insert size with the following minor modifications: only half of the library is subjected to a 15 cycle PCR in the final library amplification step. Sequence-libraries of each sample were equimolarly pooled and sequenced on 2 NextSeq500 flow-cells at 1x75 bp with a v2 high-output kit.

treatment_protocol: Steady state mice were used - no treatement

value: Spleen

tag: state

value: Steady State


title: Sth1td Sth1WT nucleosome 2

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

description: MNase-digested mononucleosome

data_processing:
De-multiplexed Fastq files from the Illumina pipeline were aligned to the Saccharomyces cerevisiae genome release 64 (UCSC SacCer3) using Novoalign version 2.8 (http://www.novocraft.com), allowing for one random repeat, base recalibration, and a minimum alignment quality score of 13. Alignments were converted to sorted, indexed Bam files using samtools.
Nuclosome coverage maps were generated from the single-end alignments using the BioToolBox program bam2wig (https://github.com/tjparnell/biotoolbox). Alignments were shifted towards to 3' end by an empirically determined size using the --shift option. Both single point enumeration (representing the predicted nucleosome midpoint) and coverage (representing the coverage of the entire predicted nucleosome fragment) wig files were generated using either the --pos option of start or extend, respectively. Reads were normalized to Reads Per Million mapped (RPM) with the --rpm option. Wig files were converted to the UCSC bigWig format for visualization and data analysis.
Genome_build: SacCer3
Supplementary_files_format_and_content: Two bigWig files are provided for each replicate, representing either normalized nucleosome midpoint counts, or normalized nucleosome coverage.

organism: Saccharomyces cerevisiae

source_name: Sth1td Sth1WT nucleosome 2

growth_protocol: Yeast cultures were grown in 100 ml synthetic complete media lacking uracil and 25% normal concentration of methionine and cysteine and supplmemented with 1% raffinose and 50 mM CuSO4. Cultures were grown at 27C with agitation until an optical density of 0.8 was achieved. Galactose was added to the media to 1% final concentration to induce UBR1 expression. After 1 hour of induction, the incubator was shifted to 37C to induce Sth1 protein degradation. After 2 hours of high temperature, cells were harvested. Cells were crosslinked for 20 minutes by addition of formaldehyde to 1% final concentration in the media and quenched by the addition of 1M glycine to 0.1M final concentration. Cells were harvested by centrifugation and washed twice with Tris-Buffered Saline. Cells were stored at -80C until preparation.

extract_protocol:
Cells (equivalent to 50 ml culture) were suspended in spheroplasting solution (1M sorbitol, 10 mM Tris pH 7.5, 10 mM 2-MercaptoEthanol, protease inhibitors) and incubated with prepared zymolyase (Sigma) at 37C until the optical density of a 1:100 dilution in 1% SDS dropped to 0.01. Spheroplasts were gently harvested by low-speed centrifugation and stored on ice until ready. Spheroplasts were resuspended with MNase Digestion buffer (50 mM Tris pH 7.5, 100 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.1% Triton X-100), split into three tubes, and digested with increasing amounts of MNase at 37C for 8 minutes. The amount of MNase was empirically determined to yield a distribution of mono-, di-, and tri-nucleosomes. MNase digestion was stopped by the addition of 0.1X volumes of stop solution (250 mM EDTA. 5% SDS). Proteinase K was added to the samples, incubated at 37C for 2 hours, and then 65C overnight to reverse cross links. Protein was precipitated from the samples by addition of 8M potassium acetate to 1.2M final concentration, cooling on ice, and centrifugation. DNA was recovered by ethanol precipitation. Samples were treated with RNAase and electrophoresed on a 1.2% agarose gel. Mononucleosomal DNA was excised from the sub-sample whose level of digestion generated an appropriate digestion pattern (about 60% mono, 30% di, and 10% tri) and purified using a Qiagen Gel Extraction Kit.
Mononucleosome DNA was phosphorylated with T4 kinase (NEB) prior to ligation of adaptors using Illumina Tru-Seq library construction kit according to manufacturers instructions. No other end repair was performed (fill-in, etc). After limited PCR amplification, samples were size selected on agarose gel and fragments corresponding to mononucleosomes were excised and purified.

tag: plasmid

value: sth1d::STH1td Gal-UBR STH1-2xFLAG


title: Sth1td nucleosome 2

description: MNase-digested mononucleosome

source_name: Sth1td nucleosome 2

value: sth1d::STH1td Gal-UBR


title: Sth1td sth1-dDL nucleosome 2

description: MNase-digested mononucleosome

source_name: Sth1td sth1-dDL nucleosome 2

value: sth1d::STH1td Gal-UBR sth1-dDL-2xFLAG


title: cDC2 KO CRE+ 3

description: cDC2s from CD11cCRExZeb2fl/fl number 3


title: Sth1td sth1-L392P nucleosome 2

description: MNase-digested mononucleosome

source_name: Sth1td sth1-L392P nucleosome 2

value: sth1d::STH1td Gal-UBR sth1-L392P-2xFLAG


title: Sth1td sth1-dDL nucleosome 1

description: MNase-digested mononucleosome

source_name: Sth1td sth1-dDL nucleosome 1


title: Sth1td sth1-L392P nucleosome 1

description: MNase-digested mononucleosome

source_name: Sth1td sth1-L392P nucleosome 1


title: cDC2 KO CRE+ 2

description: cDC2s from CD11cCRExZeb2fl/fl number 2


title: Sth1td Sth1WT nucleosome 1

description: MNase-digested mononucleosome

source_name: Sth1td Sth1WT nucleosome 1


title: cDC2 KO CRE- 1

description: cDC2s from Zeb2fl/fl number 1


title: cDC2 KO CRE+ 1

description: cDC2s from CD11cCRExZeb2fl/fl number 1


title: Sth1td nucleosome 1

description: MNase-digested mononucleosome

source_name: Sth1td nucleosome 1


title: cDC2 KO CRE- 2

description: cDC2s from Zeb2fl/fl number 2


title: cDC2 TG CRE+ 2

description: cDC2s from CD11cCRExR26-Zeb2Tg/Tg number 2


title: cDC2 TG CRE+ 4

description: cDC2s from CD11cCRExR26-Zeb2Tg/Tg number 4


title: cDC2 TG CRE+ 3

description: cDC2s from CD11cCRExR26-Zeb2Tg/Tg number 3


title: cDC2 TG CRE+ 1

description: cDC2s from CD11cCRExR26-Zeb2Tg/Tg number 1


title: cDC2 TG CRE- 2

description: cDC2s from R26-Zeb2Tg/Tg number 2


title: cDC1 KO CRE+ 2

description: cDC1s from CD11cCRExZeb2fl/fl number 2


title: cDC1 TG CRE+ 3

description: cDC1s from CD11cCRExR26-Zeb2Tg/Tg number 3


title: cDC1 TG CRE+ 4

description: cDC1s from CD11cCRExR26-Zeb2Tg/Tg number 4


title: cDC1 TG CRE+ 2

description: cDC1s from CD11cCRExR26-Zeb2Tg/Tg number 2


title: cDC1 KO CRE- 2

description: cDC1s from Zeb2fl/fl number 2


title: cDC1 KO CRE- 1

description: cDC1s from Zeb2fl/fl number 1


title: cDC1 KO CRE+ 1

description: cDC1s from CD11cCRExZeb2fl/fl number 1


title: cDC2 TG CRE- 1

description: cDC2s from R26-Zeb2Tg/Tg number 1


title: cDC1 KO CRE+ 3

description: cDC1s from CD11cCRExZeb2fl/fl number 3


title: cDC1TG CRE+ 1

description: cDC1s from CD11cCRExR26-Zeb2Tg/Tg number 1


title: cDC1 TG CRE- 2

description: cDC1s from R26-Zeb2Tg/Tg number 2


title: cDC1 TG CRE- 1

description: cDC1s from R26-Zeb2Tg/Tg number 1


title: cDC1 KO CRE+ 4

description: cDC1s from CD11cCRExZeb2fl/fl number 4


title: BURN_IP

data_processing:
Alignment: STAR aligner (version star/2.3.0e) and samtools
Mapping: Mapped to Ensembl Mus musculus mm10 genome (version GRCm38)
Counts: Generated using HTSeq_count in the HTSeq package
Genome_build: mm10
Supplementary_files_format_and_content: .txt files, tab-delimited.

source_name: Burn injury_DRG neurons

extract_protocol:
Whole DRGs were removed and immediately put into RNALater and cut into pieces in RNA later. RNA was extracted using the Rneasy Mini kit (Qiagen)
RNA libraries were prepared using TruSeq stranded total RNA library preparation.

tag: gender

value: male

value: 6-8 weeks

tag: sample group

value: three days after the burn injury

value: L3, L4, L5 whole DRG neurons


title: Control-2

source_name: Control_DRG neurons

tag: strain

tag: age

value: control


title: Burn-2

tag: genotype/variation


title: 3691_RBPJ

city: Cleveland

first: Tyler

middle: E

last: Miller

state: Ohio

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Sequencing of H3K27ac and RBPJ ChIP and an unenriched chromatin control library (input) was performed on a NextSeq, with read lengths of 50bp
Reads were aligned to hg19 using BWA (Li, et. al., 2009)
Identical ChIP-seq sequence reads were collapsed to a single read to avoid PCR duplicates.
Peaks were called using HOMER v4.6 (Heinz, et. al., 2010) using matched inputs with the following parameters : H3K27ac, –histone –tagThreshold 50; RBPJ, –factor .
Genome_build: Hg19
Supplementary_files_format_and_content: Peak file (bed file) and bigwig file was generated for each sample by HOMER v4.6.

source_name: Primary Patient Derived Tumor Model

growth_protocol: Cells were cultured in Neurobasal medium supplemented with B27, L-glutamine, sodium pyruvate (Invitrogen, Waltham, MA), 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF) (R&D Systems, Minneapolis, MN)

extract_protocol:
For histone modification and transcription factor ChIP-Seq, 2 million cells (H3K27Ac) or 10 million cells (RBPJ) were crosslinked in PBS + 1% fresh formaldehyde for 10 minutes at 37 C, quenched for 5 minutes with 125 mM glycine, washed twice in cold PBS with protease inhibitors (complete PI, Roche), and stored at -80 C. Pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g , resuspended in cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes, sonicated to an average fragment size of 200-400 bp on a Branson sonifier, and cleared of debris by centrifugation. Samples were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 0.25% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4 C overnight with 2-5 ug of antibody towards H3K27ac (Abcam, ab4729) or RBPJ (Abcam, no. 25949 ). Antigen-antibody complexes were collected with protein G Dynabeads (Life technologies) for 4 hours at 4 C, and sequentially washed with RIPA buffer (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 140 Mm NaCl), RIPA/High salt (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 360 mM NaCl), LiCl Wash Buffer (250mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.0), and TE Buffer (10mM Tris-HCl pH 8.0, 1mM EDTA). Beads were resuspended in Low SDS ChIP elution buffer (10mM Tris-HCl pH 8.0, 0.5M EDTA, 300mM NaCl, 0.1% SDS, 5mM DTT) and incubated for 6 hours at 65 C to elute DNA and reverse crosslinking. Samples were treated with RNAase for 30 minutes and proteinase K for 2 hours at 37 C. ChIP DNA was then purified from supernatants with AMPure beads (Beckman-Coulter). Input DNA was prepared in parallel by adding unenriched, diluted chromatin directly into the elution / reverse crosslinking step.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated to barcoded illumina adaptors (Quick T4 DNA ligase, NEB). Each reaction was followed by clean-up with AMPure beads (Beckman-Coulter). Ligation products were amplified by PCR for 14-18 cycles with illumina primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection or gel purification (E-Gel SizeSelect 2%, Life technologies).

tag: tumor model

tag: antibody

value: Abcam ab25949


title: 3691_H3K27Ac

value: Abcam ab4729


title: Control-1


title: 4121_RBPJ input

value: input


title: Control-3


title: 3691_H3K27Ac input


title: 4121_RBPJ


title: NOMO-1_Input_ChIPSeq

city: Cold Spring Harbor

first: Anja

middle: Fides

last: Hohmann

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: ChIP-Seq

data_processing:
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using bowtie with default parameters.
To call the peaks, MACS 1.4.2 software was used.
To generate density maps, all Brg1 peaks with an FDR <0.05% and a minimal fold enrichment of 5 over input were used. Heatmaps matrices were created by counting tags using 20 kb windows with 50 bp bins. Heatmap matrices were visualized by Java TreeView 1.1.6r4.
To generate hockeystick plots of Brd9 peaks in RN2 cells, peaks were called using MACS 1.4.2 software with a 50bp shift size and all peaks with a FDR <25% and a minimal fold enrichment of 3.5 over input were used.
To quantify FLAG-BRD9 and Brg1 chromatin occupancy after BI-7273 treatment, high confidence peaks (FDR <10%, minimal fold enrichment of 10 over input) were identified among DMSO treated RN2 FLAG-BRD9 and untransduced RN2 cells. Tag counts for these locations were then re-calculated from uniquely mapped reads in both, DMSO and BI-7273 treated samples, and normalized to the total number of uniquely mapped reads in each data set. Changes in occupancy after BI-7273 treatment were then quantified as the fold change of normalized tag counts between BI-7273 and DMSO treated samples for each of the identified high confidence peaks. To exclude regions of minimal occupancy, peaks with tag counts between 40 and 200 were excluded from the analysis of FLAG-BRD9 and Brg1 binding alterations, respectively.
Genome_build: murine: mm9, human: hg19
Supplementary_files_format_and_content: peak information was generated by MACS software

growth_protocol: Cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with appopriate sizes were prepared for sequencing.
These libraries were made following the instructions of illumina Truseq DNA sample prep kit v2.

treatment_protocol: To assess changes in chromatin binding upon BI-7273 treatment, cells were cultured in DMSO or BRD9 inhibitor for 24 hours before harvest.

value: Acute myeloid leukemia

tag: treatment


title: Burn-1

value: wild type


title: 3691_RBPJ input


title: HeLa BI-7273 2

description: Samples24-27_Hela_DMSO_vs_BI2_Rep1_2.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to mouse (mm9) or human (hg19) genome using Tophat with default parameters.
Cuffdiff software was used to compare gene expression profiles by calculting Fragments Per Kilobase of exon per Megabase of library size (FPKM) for each sample.
For biological replicates of shRNA experiments, two - three individual shRNAs were used. For BRD9 inhibitor assessement, all experiments were performed with two independent biological replicates
To define the expressed genes in further analysis of PolyA+ RNA-Seq, only the genes with FPKM≥5 in the control samples and FPKM>0 in the test samples were considered.
Processed data files contain a list of filtered genes with log-transformed fold change  of averaged FPKM values from two-three independent hairpins (shRNA experiments) or two biological replicates (inhibitor experiments) to their respective negative controls.
Genome_build: mouse: mm9; human: hg19
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for samples

source_name: HeLa

growth_protocol: Leukemia cell cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep. Fibroblasts and HeLa cells were cultured in DMEM supplemented with 10% FBS, 1% Pen/Strep.

extract_protocol:
Total RNAs were extracted using Trizol reagent.
These libraries were prepared following the instructions of illumina Truseq RNA sample prep kit v2.

treatment_protocol: To define genes affected by BRD9 knockdown, cells which express dox-inducible shRNAs were cultured with Doxycyclin for 48 hour before harvest. To define genes affected by BRD9 inhibitor treatment, cells were cultured in DMSO or BRD9 inhibitor for 24 hours before harvest.

value: Cervical cancer

value: BRD9 inhibitor


title: HeLa DMSO 2

value: DMSO


title: NOMO-1_BRD9_A303-781A_ChIPSeq

description: ChIP-Seq

value: BRD9 (A303-781A; Bethyl)


title: HeLa BI-7273 1


title: MV4-11 BI-7273 2

description: Samples20-23_MV4-11_DMSO_vs_BI2_Rep1_2.txt


title: HeLa DMSO 1


title: MV4-11 DMSO 1


title: MV4-11 DMSO 2


title: MV4-11 BI-7273 1


title: HL60 BI-7273 2

description: Samples16-19_HL60_DMSO_vs_BI2_Rep1_2.txt

value: Myc amplification


title: HL60 DMSO 1


title: HL60 DMSO 2


title: HL60 BI-7273 1