title: Cysteamine replicate 3

city: Cambridge

first: Natasha

last: Patel-Murray

state: Massachusetts

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

data_processing:
Adapter sequences were trimmed from sequencing reads using Trimmomatic-0.36.
Reads were aligned to the GRCm38.p5 transcriptome (https://www.gencodegenes.org/mouse/release_M12.html) and quantified using RSEM to create the counts matrix.
DESeq2 was used to remove the collection day and time batch effects from the counts matrix for clustering and differential analysis.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: RNA_Seq_Normalized_Abundance.txt is a matrix of normalized abundance measurements of the gene counts for each sample (compound names are abbreviated and numbers 1-3 refer to replicates).

source_name: Striatal progenitor cells

growth_protocol: Cells were seeded at 33°C with 5% CO2 and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin. After 24 hours, treatments were applied.

extract_protocol:
RNA was extracted from compound- or vehicle-treated cells in triplicate using Zymo Research Quick-RNA™ MiniPrep (Plus) kit (Zymo Research R1058) and RIN values were tested using Advanced Analytical. All samples had RIN values greater than 0.85.
Libraries were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs E7420L) and NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (New England Biolabs E7490L). Libraries were multiplexed and sequenced on an Illumina Hi-Seq 2000 for single-end 50bp reads.

treatment_protocol: STHdh cells were incubated in serum-free medium with a compound or vehicle control for 24 hours.

value: mutant (STHdhQ111)

tag: collection day

tag: collection time

value: serum starvation with 250 uM cysteamine


title: cDNA6411_7183_KC

status: Public on Jan 22 2020

type: SRA

city: Dallas

first: Uthra

last: Balaji

state: Texas

address: 3434 Live Oak St

department: Biostatistics Core

country: USA

institute: Baylor Scott & White Research Institute

library_source: transcriptomic

data_processing:
RNAseq reads trimmed and aligned to mouse genome
Normalization and differential gene  expression (DGE) analysis was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file includes normalized counts

molecule: polyA RNA

organism: Mus musculus

source_name: epidermis

extract_protocol:
Total RNA was isolated from cell lysates using the RNeasy Micro Kit (Qiagen) including on column DNase digestion. Total RNA was analyzed for quantity and quality using the RNA 6000 Pico Kit (Agilent).
Poly-A enriched NGS library construction was performed using the KAPA mRNA Hyper Prep Kit (KAPA Biosystems) using 50ng of input total RNA according to manufacturer’s protocol using 16 amplification cycles. Quality of the individual libraries was assessed using the High Sensitivity DNA Kit (Agilent). Individual libraries were quantitated via qPCR using the KAPA Library Quantification Kit, Universal (KAPA Biosystems) and equimolar pooled. Final pooled libraries were sequenced on an Illumina NextSeq 500 with paired-end 75 base read lengths

tag: condition

value: DTA

value: KC

tag: gender

value: female


title: cDNA6410_7182_KC

value: WT


title: HSC:MSC 1:1 med 3

type: protein

city: Urbana

first: Aidan

last: Gilchrist

state: IL

address: 1206 W Gregory Dr., suite 2200

institute: University of Illinois at Urbana-Champaign

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.6

hyb_protocol: not provided

scan_protocol: The microarrays were sent to Raybiotech for imaging. URL=Http://www.perkinelmer.com/microarray .  Wavelength = 532. Velocity=35 l/s. laserPower=5.0. PMTGain=1.7976931348623157E308.

data_processing:
Fluorescence signal with background subtraction were translated to qualitative cytokoine concentrations via standard curve. Standard curves were generated by using the standard curve dilution with known concentrations. Outliers within the standard curve were deleted to improve R value.  Standard 3 was included on each slide to act as a normalization factor. Quantitative concentration results were extracted from the raw data using Q-analyzer software (Analysis Tool for QAM-CAA-4000, RayBiotech) with concentration values set within limits of detection.
Valeus are the concentration of the cytokine in pg/mL. These are extracted from the raw data using Q-analyzer software (Analysis Tool for QAM-CAA-4000, RayBiotech) with concentration values set within limits of detection.

label: Cy-3 equivalent dye-conjugated streptavidin

molecule: protein

source_name: co-cuture HSC:MSC,1:1, med hydrogel

label_protocol: In brief, each well of the microarray was blocked and washed prior to incubation with 100 µL of sample overnight. The wells were then washed, incubated with a biotinylated antibody cocktail, and then incubated with a Cy3 equivalent dye-streptavidin. Each microarray also included a standard curve dilution for later quantitative analysis.

growth_protocol: HSPCs and MSPCs were cultured at increasing ratios of 1:0, 1:1, 1:10, 0:1, 0:10 (HSPCs:MSPCs) in 4, 5, 7.5 wt% methacrylamide-functionalized gelatin (GelMA) (49, 50) at constant crosslinking conditions (85% functionalization, 0.1% lithium acylphosphinate photoinitiator (PI), and 7.14 mW/cm2 UV light for 30 seconds). HSPC seeding density was kept constant at 1x105 HSPCs/mL, and cells were encapsulated in 5mm diameter hydrogels (20 µL) and cultured for 7 days in 300 µL SFEM media (#09650 Stemcell Technologies) supplemented with 100 ng/mL SCF (#250-03, Peprotech) and 0.1% PenStrep, changed every 2-days.

extract_protocol: Media was collected from each sample at day 2, 4, and 6 and store at -80°C for future use.

tag: day media collected

tag: gelma wt%

tag: hsc

value: MSC seeding ratio (HSC=1x10^5 cells/mL):1:1

tag: block number in micrarray


title: ES_POLR3G_ChIPseq

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: ChIPed genomic DNA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 murine genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best".
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq.
peak calling performed using MACS (RNA Pol II) or HOMER package (POLR3C, POLR3G, and POLR3GL)
Genome_build: mm9
Supplementary_files_format_and_content: Tiled data files (TDF) for input and ChIP samples.

molecule: genomic DNA

growth_protocol: ES-E14TG2a cells were cultured on 0.1% gelatinized tissue-culture plates in complete ESC growth medium (Gibco) supplemented with LIF and 10% ES-certificated fetal bovine serum at 37 °C. Primary MEFs were derived from E12.5 embryos, maintined in ESC growth medium supplemented with 10% FBS (without LIF), and passaged 3 to 5 times prior to ChIP-seq analyses.

extract_protocol:
Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with ~10 ug of indicated antibodies and 100 μL Dynal protein G matrix. ChIPed DNA fragments were recovered using a PCR purification kit from Qiagen and ~10 ng DNA were submitted to the Epigenomic Core Facility at Weill Cornell Medical Colleage for library construction and high throughput sequencing.
Multiplexing libraries were prepared for sequencing using Illumina TruSeq Rapid SR Cluster Kit according to the standard protocol.

treatment_protocol: Cells were fixed and harvested at 80% confluency. For each ChIP-seq assay, 30-50 million E14tg2A or primary MEFs were used. Chromatin was prepared from isolated nuclei and sonicated to an average size of 200 ~700 bp in FA lysis buffer (50 mM Hepes, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1 % SDS, 0.1 % Na-deoxycholate, and 1X Complete protease inhibitor [Roche])

tag: cell type

value: Embryonic Stem Cell

tag: biomaterial provider

value: ATCC CRL-1821

tag: chip antibody

value: anti-POLR3G, in-house antibody, Roeder Lab


title: Cysteamine replicate 2

tag: strain

tag: genotype

tag: treatment


title: HSC:MSC 1:1 low 3

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.3

source_name: co-cuture HSC:MSC,1:1, low hydrogel


title: HSC:MSC 1:1 med 2

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.5


title: cDNA6414_7186_KC


title: Input_Rep2

city: La Jolla

first: Tomas

last: Duffy

state: CA

address: 10550 N Torrey Pines Rd

institute: TSRI

data_processing:
ChIP-seq tags of FoxO1 were aligned against the reference human genome hg19 using Bowtie2
peaks were called using PePr
Genome_build: hg19

organism: Homo sapiens

source_name: Input

growth_protocol: 10^6 freshly isolated chondrocytes were plated on a 15 cm dish and cross-linked when 90% confluent.

extract_protocol:
FoxO1-DNA complexes were isolated with antibody.
For library preparation, 10 ng of each sample was prepared using the NEB Ultra DNA Library Prep Kit for Illumina following manufacturer’s instructions.

tag: donor status

value: total knee replacement surgery patient

value: primary chondrocytes


title: Cysteamine replicate 1


title: HSC:MSC 1:1 med 1

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.4


title: ES_POLR3GL_ChIPseq

description: ChIPed genomic DNA

value: anti-POLR3GL, in-house antibody, Roeder Lab


title: Input_Rep1


title: HSC:MSC 1:1 low 2

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.2


title: Pizotifen replicate 3

value: serum starvation with 5uM pizotifen


title: HSC:MSC 1:1 low 1

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.1


title: Pizotifen replicate 2


title: HSC:MSC 1:1 high 2

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.8

source_name: co-cuture HSC:MSC,1:1, high hydrogel


title: Pizotifen replicate 1


title: FoxO1_ChIP-seq_Rep2


title: FoxO1_ChIP-seq_Rep1


title: HSC:MSC 1:0 high 3

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
1.9

source_name: co-cuture HSC:MSC, 1:0, high hydrogel

value: MSC seeding ratio (HSC=1x10^5 cells/mL):1:0


title: HSC:MSC 1:0 high 2

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
1.8


title: Haloperidol replicate 2

value: serum starvation with 0.5nM haloperidol


title: HSC:MSC 1:0 high 1

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
1.7


title: Haloperidol replicate 1


title: SW480-N

city: Guangzhou

first: Shengyuan

state: Guangdong province

address: No. 1023-1063, shatai South Road, Baiyun District, Guangzhou, Guangdong Province

department: Gastroenterology

country: China

institute: Nanfang Hospital, Southern Medical 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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

source_name: Colorectal cancer cell line

extract_protocol:
Cells were washed twice and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: tissue

value: Colorectal cancer cell line

value: wild type


title: Fingolimod phosphate replicate 3

value: mutant (STHdhQ111)

tag: collection day

value: serum starvation with 250nM fingolimod phosphate


title: HSC:MSC 1:0 med 3

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
1.6

source_name: co-cuture HSC:MSC, 1:0, med hydrogel


title: Fingolimod phosphate replicate 2

tag: collection time


title: HSC:MSC 1:0 med 2

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
1.5


title: FoxO1_ChIP-seq_Rep3


title: Fingolimod phosphate replicate 1


title: HSC:MSC 1:0 med 1

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
1.4


title: Nortriptyline replicate 3

value: serum starvation with 1nM nortriptyline


title: HSC:MSC 1:0 low 3

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
1.3

source_name: co-cuture HSC:MSC, 1:0, low hydrogel


title: RKN RNA-seq

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

description: RNA-seq of a human leiomyosarcoma cell line.

data_processing:
RNA-seq data were aligned using STAR with expression quantification using Cufflinks to generate gene expression values in FPKM units.
Genome_build: hg19
Supplementary_files_format_and_content: Processed RNA-seq data files with FPKM values are in text format

source_name: Leiomyosarcoma cell line

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen).
Libraries for Illumina NextSeq 500 sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced with single-end 75 bp reads.

value: RKN


title: Nortriptyline replicate 2


title: HSC:MSC 1:0 low 2

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
1.2


title: SKLMS1 RNA-seq


title: Haloperidol replicate 3


title: HSC:MSC 1:0 low 1

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
1.1


title: SW620-N


title: 22RV1-DHT-DMSO-input

city: North Chicago

first: Josh

last: Plotnik

address: 1 North Waukegan Rd, AP10/210A

institute: AbbVie Inc.

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the human genome (hg19) using the BWA algorithm
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated from BedGraph to BigWig. Scores represent peak density.

source_name: 22RV1 immortalized prostate cancer cell line

growth_protocol: LNCaP-FGC or 22RV1 cells were grown for 72 hrs in charcoal stripped (steroid free) serum,

extract_protocol:
Lysates were clarified from sonicated, fixed cell pellets and protein-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

treatment_protocol: Cells were pretreated with indicated inhibitors for 45 minutes followed by 24 hr stimulation with 5 nM DHT

value: input

tag: agent

value: DMSO + 5 nM DHT, 6 hrs


title: Nortriptyline replicate 1


title: 22RV1-DHT-DMSO_H3K27Ac

value: H3K27Ac (Active Motif, Cat 39133)

value: 22RV1 immortalized prostate cancer cell line


title: SacCer.3CellCycle.Replicate.2

city: Aurora

first: Joshua

middle: C

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

description:
Yeast CDK bypass
SacCer.3CellCycle.merged.bedgraph

data_processing:
Yeast fastq files were aligned to SacCer3 using bowtie3
The resulting sam files were turned into bams and duplicate reads were removed using samtools
Bam files were turned into bedgraphs using the bedtools2.29.3
If samples were sequenced for additional depth, the bam files were merged at this point
Bedgraphs were read count normalized using an RPM calculation
RPM normalized bedgraphs were then scaled to mitochondria read percentages
The fully normalized bedgraphs were binned to 100bp and smoothed using a 10kb sliding window
To make the final processed files, replicates were merged and averaged to make a single bedgraph
Genome_build: SacCer3
Supplementary_files_format_and_content: Bedgraph normalized by RPM and mitochondria content, merged across replicates
Library strategy: Rerep-seq

organism: Saccharomyces cerevisiae

source_name: in vitro cell culture

growth_protocol: Yeast strains were grown according to standard procedures in YPD (yeast extract, peptone, and 2% dextrose) at 30ºC

extract_protocol:
DNA extraction: As RerepSeq selectively fragments rereplicated DNA and enriches those sequences by size selection, it is imperative that the genomic input DNA is of high molecular weight. For yeast samples: cells were pelleted by centrifugation at 3000 rpm for 3 minutes and resuspended in SCE (1M sorbitol, 100 mM sodium citrate, 10 mM EDTA pH 8.0); fresh 0.125% (v/v) β-mercaptoethanol and 10 U/mL zymolyase was added and incubated for 30-60 minutes at 37ºC to digest cell walls; human cells or yeast spheroplasts were pelleted by centrifugation at 3000 rpm for 3 minutes and resuspended in 500uL RIPA buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 140 mM NaCl, 1 mM PMSF) with RNase A, 0.2 mg/mL and incubated at 37ºC for 1 hour. 25uL 20% SDS and 10µl of 20 mg/ml proteinase K was then added and allowed in incubate at 55ºC for 2 hours. DNA was extracted twice using Phenol:Chloroform:Isoamyl alcohol (25:24:1, v/v) and precipitated using isopropanol.  DNA was resuspended and stored in nuclease free water. RerepSeq Digestion: In an 8 strip 200 µl PCR tube 1 – 5 µg (depending on the experiment) high molecular weight genomic DNA was mixed with 2.5uL 10X Hoechst 33258 (0.1mg/ml) and 2.5uL 10X NEB Buffer 4 (50 mM Potassium Acetate, 20 mM Tris-acetate , 10 mM Magnesium Acetate, 1 mM DTT pH 7.9@25°C) to a final volume of 24uL; open tubes placed upright in PCR tube rack, covered with glass plate (3" x 3" glass plate from VWR Vertical Gel Electrophoresis Systems), exposed to 7.5 minutes of glass plate filtered (UVA only) from a Stratalinker.  Following UVA treatment,  samples were digested with 0.5uL UDG (5 units of Uracil-DNA Glycosylase), 0.5uL APE1 (10 units of human apurinic/apyrimidinic endonuclease 1) for 2 hours at 37C. Digested DNA was repaired with NEB’s FFPE DNA Repair Mix for 30 minutes then separated on 0.8% agarose gel for 15 minutes.  Fragmented DNA ranging from 0.1Kb to 3Kb was gel extracted with Wizard® SV Gel and PCR Clean-Up System (Promega) and the purified DNA was resuspended in 50uL of water for subsequent qPCR and sequencing analysis.
Illumina Nextera DNA Flex Library Prep Kit

treatment_protocol: Cells were grown in YP 2% raffinose to an OD600 of 0.5, arrested in G1 with α-factor (100 ng/ml) for 2 hours. 0.1mM BrdU was added and the culture was split into two, with 2% galactose added to one for induction of cdc45 H22Y and sld2-11D, while the other was maintained in 2% raffinose. Samples were collected at 0 and 5 hours for flow cytometry and DNA extraction

value: MATa ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 bar1::hisG ars608{delta}::HIS3 ars609{delta}::TRP1 ars305::TRP1 GPD-HSV-TK ADH1-hENT1 BrdU-Inc


title: Nicotinamide replicate 3

value: serum starvation with 0.5nM nicotinamide


title: 22RV1-DHT-ABBV-744_BRD4

value: 90 nM ABBV-744 + 5 nM DHT, 6 hrs


title: SKUT1 RNA-seq


title: 22RV1-DHT-ABBV-075_BRD4

value: 60 nM ABBV-075 + 5 nM DHT, 6 hrs


title: SKN RNA-seq

value: SKN


title: SacCer.3CellCycle.Replicate.1


title: SacCer.cdkByPass.Galacose.Replicate3

description:
Yeast CDK bypass
SacCer.cdkByPass.Galacose.merged.bedgraph

value: MATa ade2-1 ura3-1 his3-11,15::HIS3 GPD-HSV-TK ADH1-hENT1 BrdU-Inc trp1-1 leu2-3,112 can1-100 {delta}bar1::hisG CDC45 H22Y ura3-1::GAL-sid2-11D-MHT (URA3) leu2-3,112::GAL-DBF4-MHT (LEU2)


title: Nicotinamide replicate 2


title: 22RV1-DHT-DMSO_BRD4


title: HSC:MSC 0:0

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
media

organism: synthetic construct

source_name: SFEM media

value: day 0

value: MSC seeding ratio (HSC=1x10^5 cells/mL):0


title: LNCaP-DHT-DMSO_AR 90 nM ABBV-744 + 5 nM DHT, 6 hrs

source_name: LNCaP-FGC immortalized prostate cancer cell line

value: AR (Santa Cruz, Cat SC-13062)

value: LNCaP-FGC prostate adenocarcinoma cancer cell line


title: Diacylglycerol kinase inhibitor II replicate 3

description: Diacylglycerol_kinase_inhibitor_II_rep3_STHdhQ111

value: mutant (STHdhQ111)

value: serum starvation with 10uM diacylglycerol kinase inhibitor II


title: SacCer.cdkByPass.Galacose.Replicate1


title: LNCaP-DHT-DMSO_AR 60 nM ABBV-075 + 5 nM DHT, 6 hrs


title: SacCer.cdkByPass.Galacose.Replicate2


title: Diacylglycerol kinase inhibitor II replicate 2

description: Diacylglycerol_kinase_inhibitor_II_rep2_STHdhQ111


title: LNCaP-DHT-DMSO_AR DMSO + 5 nM DHT, 6 hrs


title: Diacylglycerol kinase inhibitor II replicate 1

description: Diacylglycerol_kinase_inhibitor_II_rep1_STHdhQ111


title: SacCer.cdkByPass.Rafinose.Replicate3

description:
Yeast CDK bypass
SacCer.cdkByPass.Rafinose.merged.bedgraph


title: Trichostatin A replicate 3

value: serum starvation with 10nM trichostatin A


title: SacCer.cdkByPass.Rafinose.Replicate2


title: SacCer.cdkByPass.Rafinose.Replicate1


title: SacCer.RepTiming.80min.Replicate3

description:
Yeast replication samples
SacCer.RepTiming.80min.merged.bedgraph

data_processing:
Yeast fastq files were aligned to SacCer3 using bowtie2
The resulting sam files were turned into bams and duplicate reads were removed using samtools
Bam files were turned into bedgraphs using the bedtools2.29.2
If samples were sequenced for additional depth, the bam files were merged at this point (see SacCer.RepTiming data, replicates 1a and 1b)
Bedgraphs were read count normalized using an RPM calculation
RPM normalized bedgraphs were then scaled to mitochondria read percentages
The fully normalized bedgraphs were binned to 100bp and smoothed using a 10kb sliding window
To make the final processed files, replicates were merged and averaged to make a single bedgraph
Genome_build: SacCer3
Supplementary_files_format_and_content: Bedgraph normalized by RPM and mitochondria content, merged across replicates
Library strategy: Rerep-seq

treatment_protocol: For the synchronized replication timing experiment, yeast cells were arrested in G1 with α-factor (100 ng/ml) for 2 hours, then released into fresh media containing (amount) 0.1mM BrdU to label one DNA strand. To maintain synchronization the culture was arrested with α-factor a second time, 40 minutes post release. This second G1 arrested culture was released again into media containing 0.1mM BrdU and 50 μg/ml pronase,   flow and DNA samples were collected to monitor S-phase progression.


title: Trichostatin A replicate 2


title: Selisistat replicate 3

value: serum starvation with 10uM selisistat


title: Trichostatin A replicate 1


title: SacCer.RepTiming.35min.Replicate3

description:
Yeast replication samples
SacCer.RepTiming.35min.merged.bedgraph


title: Selisistat replicate 2


title: Nicotinamide replicate 1


title: Infected AO rep 3

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

data_processing:
Bases were called using the Real Time Analysis 2 software of the NextSeq500.
Reads were trimmed for low quality and adaptor sequences using Trimmomatic (0.36) using the following parameters:SE -phred33 SLIDINGWINDOW:5:20 MINLEN:20 ILLUMINACLIP: TruSeq3-SE.fa:3:30:10
Reads were mapped using STAR (2.5.2a) and filtered for uniquely mapped reads.
BAM files of multiplexed samples were merged using samtools (version 1.3).
Count tables were generated by the summarize overlaps function in the genomic alignments R package (version 1.16.0) using the "Union" parameter. Differential gene expression analysis was performed using the DESeq2 package (version 2.1.20) with the annotations from the Rice Annotation Project Database (version 38). Genes with a false discovery rate (FDR) < 0.05 were considered differentially expressed compared to the control group.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: For each sample one text file with raw counts and one text file containing gene counts normalized by DESEQ2

organism: Oryza sativa Japonica Group

source_name: infected_AO_gall tissue

growth_protocol: Seeds of wild-type rice Oryza sativa cv. ‘Nipponbare’ were obtained from USDA (GSOR-100). Different TOS17 insertional mutants in Nipponbare were obtained from the Rice Genome Resource Center of the National Institute of Agrobiological Sciences (Hirochika et al., 1996; Hirochika, 2001): a mutant in jasmonic acid amido-synthetase (Osjar1, NC2728 (Miyao et al., 2003), a mutant in GDP-mannose-3,5-epimerase (gme = vtc, ND6172; LOC_Os10g28200), known to contain 20-30% less ascorbate (Frei et al., 2012), a mutant in mannose-6-phosphate isomerase (= phosphomannose isomerase,  pmi, NF5987; LOC_Os01g03710) and a mutant in thylakoid-bound ascorbate peroxidase ASCPX8 (ascpx, ND0462; LOC_Os02g34810). Mutant lines were genotyped in T1 by triple primer PCR using gene specific primers and the TOS17-tail6 primer AGGTTGCAAGTTAGTTAAGA to produce homozygous T2 seeds. The description and the biological role of mutant is summarized in (Table S2). The expression level of the mutated gene was also checked by qRT-PCR and confirmed to be knocked-down at least 5-fold. Seeds were germinated on wet filter paper for 4-5 days at 30°C and seedlings were then transferred to SAP-substrate (Sand mixed with Absorbent Polymer AquaPerla®, DCM, Belgium) and further grown at 28oC, under a light regime of (day/night) 12/12. Hoagland solution was given as a source of nutrients 3 times a week.

extract_protocol:
Root systems were collected 3 days after nematode inoculation, which corresponds to 4 days after treatment with AO (20 U/mL). For each treatment, three independent biological replicates, containing a pool of 4-5 individual plants, were taken. RNA was extracted using the QIAGEN RNeasy Plant Mini kit according to the manufacturer’s instructions, with additional sonication after adding extraction buffer RLT. RNA integrity was checked using the Agilent BioAnalyzer 2100 (Agilent).
Approximately one microgram of total RNA was used for 3’ mRNA-Seq library construction using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina. To minimize lane effects the samples were multiplexed, using the multiplexing sequencing adapters provided in the Multiplexing Sample Preparation Oligo Kit (Illumina). Size selection of the library was performed on a 2% agarose gel (Low Range Ultra Agarose, Biorad 161-3107). The denatured library was diluted to a final concentration of 6 pM and loaded on a flow cell (Illumina). After cluster generation, the multiplexed library was sequenced on an Illumina NextSeq500 (75 cycles, single end, high output).

treatment_protocol: M. graminicola was originally isolated in the Philippines (Batangas) and was kindly provided by Dirk De Waele (Catholic University, Leuven, Belgium). A nematode culture was maintained on susceptible rice plants grown in potting soil, under light and temperature conditions as described above. Second stage juveniles (J2s) were extracted using a sieve/tray extraction method. Two weeks old plants were inoculated with 250-300 J2s per plant. Control plants were mock inoculated with water. Ascorbate oxidase (AO, 20 U/ml) was purchased from Sigma and dissolved in water and 0.02% (v/v) of Tween20 was added. Control plants were sprayed with distilled water containing 0.02% (v/v) of Tween20. In each experiment, eight two-weeks-old plants per treatment were sprayed until run-off with 50 mL of solution (at 24 h prior to nematode inoculation, in cases where infected plants were used).

tag: cultivar

value: Nipponbare

tag: plant age

value: Two weeks

tag: infection

value: Meloidigyne graminicola

value: Ascorbate oxidase (AO, 20 U/ml)

value: Gall tissue


title: SacCer.RepTiming.60min.Replicate3

description:
Yeast replication samples
SacCer.RepTiming.60min.merged.bedgraph

value: MATa ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 bar1::hisG ars608{delta}::HIS3 ars609{delta}::TRP1 ars305::TRP1 GPD-HSV-TK ADH1-hENT1 BrdU-Inc


title: Infected AO rep 2


title: SacCer.RepTiming.30min.Replicate3

description:
Yeast replication samples
SacCer.RepTiming.30min.merged.bedgraph


title: Selisistat replicate 1


title: SacCer.RepTiming.25min.Replicate3

description:
Yeast replication samples
SacCer.RepTiming.25min.merged.bedgraph


title: Infected AO rep 1


title: 4-Deoxypyridoxine replicate 2

value: serum starvation with 4mM 4-deoxypyridoxine


title: AO rep 2

value: water (mock control)

value: Root tissue


title: 4-Deoxypyridoxine replicate 1


title: AO rep 1


title: SacCer.RepTiming.15min.Replicate3

description:
Yeast replication samples
SacCer.RepTiming.15min.merged.bedgraph


title: SacCer.RepTiming.20min.Replicate3

description:
Yeast replication samples
SacCer.RepTiming.20min.merged.bedgraph


title: Loxapine replicate 3

value: serum starvation with 10uM loxapine


title: Loxapine replicate 2


title: SacCer.RepTiming.0min.Replicate3

description:
Yeast replication samples
SacCer.RepTiming.0min.merged.bedgraph


title: Infected rep 2

source_name: infected_untreated_gall tissue

value: distilled water containing 0.02% (v/v) of Tween20


title: Infected rep 3


title: Loxapine replicate 1

source_name: Striatal progenitor cells


title: SacCer.RepTiming.60min.Replicate2


title: Cyproheptadine replicate 3

value: serum starvation with 10uM cyproheptadine


title: Infected rep 1


title: 4-Deoxypyridoxine replicate 3


title: SacCer.RepTiming.30min.Replicate2


title: Cyproheptadine replicate 2


title: SacCer.RepTiming.35min.Replicate2


title: Control rep 3


title: Cyproheptadine replicate 1


title: Control rep 1


title: SacCer.RepTiming.20min.Replicate2


title: AO rep 3


title: Sodium butyrate replicate 3

value: serum starvation with 1mM sodium butyrate


title: SacCer.RepTiming.15min.Replicate2


title: Sodium butyrate replicate 2

value: mutant (STHdhQ111)


title: SacCer.RepTiming.80min.Replicate2


title: SacCer.RepTiming.0min.Replicate2


title: Sodium butyrate replicate 1


title: E_E1_R1

city: Oslo

first: Leif

middle: Christopher

last: Lindeman

state: Oslo

address: Ullevålsveien 72

country: Norway

institute: Norwegian University of Life Sciences

description: exposed for PF-06726304 acetate

data_processing:
Raw data files were mapped to GRCz11 using the bioinformatics pipeline snakePipes using the ATAC seq mode.
In this pipeline, fastq files are quality and adapter trimmed with Trimgalore, aligned with Bowtie2 and peaks are detected with MACS2. Due to too low read depths we needed to adjust the analysis by including 1 nucleosome by increasing the fragment length to 300 bp. The obtained MACs peaks from each replicate were merged, and overlapping peaks were merged to one peak.
Genome_build: GRCz11
Supplementary_files_format_and_content: MACS peaks

organism: Danio rerio

source_name: ezh2i exposed embryos

extract_protocol: The chorion was removed with pronase (0.3 mg/mL pronase) and the yolk was dissociated in 500 μL Ginzburg fish ringer deyolk buffer (55 mM NaCl, 1.8 mM KCl,1.25 mM NaHCO3) and the cell membrane was lysed in 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA630). A 2X DNA tagmentation buffer (22 mM Tris-HCl pH 7.4, 10 mM MgCl2, 20% Dimethylformamide; pH 7.4) was prepared. The isolated nuclei were resuspended in 50 μL transposition reaction mixture (25 μL DNA tagmentation buffer, 1.25 μL Tn5 (Illumina, 15027865), 23.75 μL H2O). The samples were incubated on Thermomixer at 300 rpm, 37 °C for 30 minutes. The tagmented DNA was purified with the MinElute PCR Purification Kit (QIAGEN, cat. #28004) and eluted in 10 μL elution buffer. The Nextera Index Kit (Illumina, FC-121-1030) was used for the library preparation.Real-time PCR was performed using 1 μL of the transposed DNA and 9 μL qPCR master mix (1X NEB Next High-Fidelity PCR Master Mix (New England Labs, cat. #M0541), 1X SybrGreen, 0.25 nM indexed primers) to determine the number of PCR cycles needed for the library preparation. The temperature regime for the thermocycling was (1) 72 °C for 5 minutes, (2) 98 °C for 30 seconds, (3) 98 °C for 10 seconds, (4) 63 °C for 30 seconds, and (5) 72 °C for 30 seconds. Step 3 - 5 was repeated 20 times. The preferred number of amplification cycles for the libraries was decided to be 9-10 cycles.The remaining 9 μL of purified transposed DNA was PCR amplified with 41 μL PCR master mix (1X NEB Next High-Fidelity PCR Mastermix (New England Labs, cat #M0541), 5 μM common and specific index primers (Nextera Index Kit, Illumina). The temperature regime for the thermocycling was (1) 72 °C for 5 minutes, (2) 98 °C for 30 seconds, (3) 98 °C for 10 seconds, (4) 63 °C for 30 seconds, and (5) 72 °C for 60 seconds. The amplified library was purified using the MinElute PCR Purification Kit and eluted in 20 μL of elution buffer. The libraries were cleaned up on a 2% agarose gel (Xe dry gel system, Invitrogen). During blue light excitation, the <100 bp and >15 kb localizations were removed, and the DNA libraries of interest were extruded from the gel using Invitrogen PureLink Quick Gel Extraction Kit (Invitrogen, cat. #K2100).The libraries were pair-end sequenced with a read length of 150 bases and a read depth of 50 million raw reads. The sequencing was outsourced to Novogene, Hong Kong, China.

value: AB Wild Type

tag: developmental stage

value: 5.5 hpf

value: embryo


title: E_E2_R1

description: exposed for PF-06726304 acetate


title: nGFP0hr3

city: Boston

first: Doaa

middle: AS

last: Megahed

address: 200 Longwood Avenue, Harvard Medical schooL, WaB 536D

department: Systems Biology

institute: Harvard Medical School

data_processing:
Sequence alignment was done using STAR using human genome assembly hg19
Differential expression was done using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: .txt, differentially expressed genes, isoforms and splicing isoforms as outputted by cufflinks

growth_protocol: Cells were grown in Tet-free medium with P/S and 10% Tet-compatible FBS from Clontech® until reaching confluence.

extract_protocol:
Cells were harvest in 600 ul of Qiagen's RLT lysis buffer + B-mercaptoethanol.
Library's were constucted using Takara's PrepX PolyA mRNA Isolation kit, then prepared using Illumina's PrepX™ RNAseq library reagent kit on the Apollo 324 system

treatment_protocol: Once confluence was reached, the medium was supplemented with 1ng/ml Doxycycline to induce gene expression in each cell line, while controls were recieved an equivalent volume of sterile ddH2O (solvent).

value: nGFP

tag: doxycycline treatement


title: SacCer.RepTiming.80min.Replicate1b


title: nGFP0hr2


title: E_C3_R1

description: Control

source_name: unexposed embryos


title: nGFP0hr1


title: SacCer.RepTiming.80min.Replicate1a


title: Meclizine replicate 3

value: serum starvation with 10uM meclizine


title: Meclizine replicate 2


title: Control rep 2

value: Nipponbare

value: Two weeks


title: E_C2_R1

description: Control


title: 5SA0hr2


title: Meclizine replicate 1


title: SacCer.RepTiming.60min.Replicate1b


title: SacCer.RepTiming.60min.Replicate1a


title: SacCer.RepTiming.25min.Replicate2


title: 5SA0hr3


title: E_C1_R1

description: Control


title: Q111SST replicate 3

value: serum starvation


title: E_E3_R1

description: exposed for PF-06726304 acetate


title: SacCer.RepTiming.35min.Replicate1b

value: MATa ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 bar1::hisG ars608{delta}::HIS3 ars609{delta}::TRP1 ars305::TRP1 GPD-HSV-TK ADH1-hENT1 BrdU-Inc


title: 5SA0hr1


title: Late neuritis rep3

city: Harbin

first: Yang

last: Xue

address: 23 You Zheng Street

institute: The First Affiliated Hospital of Harbin Medical University

data_processing:
Basecalls performed using bcl2fastq.
The useful Perl script was used to filter the original data (raw reads) to guarantee the data quality. The contaminated reads for adapters (read bases containing more than 5 base pairs of adapter sequences), low-quality reads (number of read bases whose phred quality value was ≤19 accounting for more than 15%), and reads whose N base value was >5% of the total bases in raw reads were removed. The contents of Q30 of clean reads were calculated. All subsequent analysis was based on clean reads.
Reference gene and genome annotation files were downloaded from the ENSEMBL website (http://www.ensembl.org/index.html). Bowtie v1.0.1 was used to build the reference genome library, and then clean reads were compared to the reference genome using HISAT2 v2.1.0. The fragments per kilobase per million mapped fragments value was calculated to estimate the expression level of genes in each sample.
Genome_build: ftp://ftp.ensembl.org/pub/release-89/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Rattus norvegicus

source_name: Sciatic nerves

extract_protocol:
Total RNA was extracted from the sciatic nerve tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA degradation and contamination were assessed by 1% agarose gel electrophoresis. RNA integrity and concentration were evaluated on a Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA) using an RNA Nano 6000 Assay Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EAN rats were subcutaneously injected at the base of the tail with 200 μL of an emulsion containing 230 μg myelin P2 peptide (amino acids 53–78; TESPFKNTEISFKLGQEFEETTADNR; GL Biochem, Shanghai, China), 2 mg Mycobacterium tuberculosis H37RA (Difco, Detroit, MI, USA), 100 μL Freund’s incomplete adjuvant (Sigma, St. Louis, MO, USA), and 100 μL saline. Control animals (sham) were injected with an inoculum containing 100 µL saline and 100 µL Freund’s incomplete adjuvant.

value: Sciatic nerves

value: Lewis

tag: gender

value: female

tag: group

value: Late neuritis


title: Q111SST replicate 2


title: Late neuritis rep2


title: Q111SST replicate 1


title: SacCer.RepTiming.35min.Replicate1a


title: SacCer.RepTiming.30min.Replicate1b


title: nGFP24hr1


title: nGFP24hr2


title: SacCer.RepTiming.30min.Replicate1a


title: Q7SST replicate 3

value: wild type (STHdh7)


title: 5SA24hr2


title: 5SA24hr1


title: Q7SST replicate 2


title: Q7SST replicate 1


title: Peak neuritis rep2

value: Peak neuritis


title: Peak neuritis rep3


title: Early neuritis rep3

value: Early neuritis


title: Q111 Meclizine

data_processing:
ChIP-Seq adapter sequences were trimmed from sequencing reads using Trimmomatic-0.36.
Reads were aligned to the mm10 genome using Bowtie2
Reads were sorted and indexed, and mitochondrial DNA was removed using samtools-1.3.
Peaks were called using MACS2 with a q-value threshold of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: We generated bed files using MACS2, which calls peak regions from alignments.

growth_protocol: Cells were maintained at 33°C with 5% CO2 and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin.

extract_protocol:
Compound- or vehicle-treated cells were crosslinked with 1% formaldehyde for 8 minutes and quenched with glycine for 5 minutes, lysed in 2X lysis buffer (50mM Tris-HCl pH8, 150mM NaCl, 1% Triton X-100, 0.1% Na Deoxycholate, 5mM CaCl2 and protease inhibitors) for 20 minutes on ice, and digested with 100u MNase (New England Biolabs M0247) for 10 minutes at 37°C. The MNase digestion was terminated by addition of 10mM EDTA. Chromatin was incubated with the anti-H3K4me3 antibody (Millipore 07-473, RRID: AB_1977252) overnight at 4°C, followed by incubation with Protein G beads (Invitrogen 10004D) for 2 hours at 4°C. The beads were washed with PBS (6x) and samples were eluted in EB (10mM Tris-HCl pH8, 5mM EDTA, 300mM NaCl, 0.1% SDS) supplemented with Proteinase K (New England Biolabs P8107S). SPRI beads were used for clean-up and yield was measured using Qubit Fluorimeter.
Libraries were prepared using NEBNExt® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs E7645S). Libraries were sequenced on an Illumina Hi-Seq 2000 for single-end 50bp reads.

value: mutant (STHdhQ111)


title: Peak neuritis rep1


title: SacCer.RepTiming.25min.Replicate1b


title: SacCer.RepTiming.25min.Replicate1a


title: Q111 Diacylglycerol kinase inhibitor II

value: serum starvation with 10uM diacylglycerol kinase inhibitor II


title: LNCaP-DHT-DMSO-input

growth_protocol: LNCaP-FGC cells were grown for 72 hrs in charcoal stripped (steroid free) serum,

value: 5nM DHT

tag: time point

value: 6 hours

tag: chip antibody

value: input

value: LNCaP-FGC prostate adenocarcinoma cancer cell line


title: SacCer.RepTiming.20min.Replicate1b

tag: genotype


title: LNCaP-DHT-DMSO_H3K27Ac

value: H3K27Ac (Active Motif, Cat 39133)


title: HSC:MSC 1:10 low 2

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
3.2

source_name: co-cuture HSC:MSC,1:10, low hydrogel

tag: day media collected

tag: gelma wt%

tag: hsc

value: MSC seeding ratio (HSC=1x10^5 cells/mL):1:10

tag: block number in micrarray


title: Q111 Loxapine

tag: strain

tag: treatment

value: serum starvation with 10uM loxapine


title: Early neuritis rep1

tag: tissue


title: Late neuritis rep1


title: Early neuritis rep2


title: SacCer.RepTiming.20min.Replicate1a

value: MATa ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 bar1::hisG ars608{delta}::HIS3 ars609{delta}::TRP1 ars305::TRP1 GPD-HSV-TK ADH1-hENT1 BrdU-Inc


title: SacCer.RepTiming.15min.Replicate1b


title: LNCaP-DHT-Enz_BRD4

tag: agent

value: 5nM DHT, 3uM Enzalutamide

tag: cell line


title: LNCaP-DHT-ABBV-744_BRD4

value: 5nM DHT, 90nM ABBV-744


title: Control rep3

value: Sciatic nerves

value: Lewis

value: female

value: Control


title: Q111 Cyproheptadine

value: serum starvation with 10uM cyproheptadine


title: LNCaP-DHT-ABBV-075_BRD4

value: 5nM DHT, 60nM ABBV-075


title: Q111SST

value: mutant (STHdhQ111)

value: serum starvation


title: SacCer.RepTiming.0min.Replicate1b


title: Control rep1


title: Q7SST

value: wild type (STHdh7)


title: LNCaP-DHT-DMSO_BRD4

value: 5nM DHT

value: 6 hours


title: SacCer.RepTiming.0min.Replicate1a


title: T lymphocytes, Sample24_RPMI_Day5

status: Public on Jan 21 2020

city: Atlanta

first: Arun

last: Boddapati

state: GA

address: 954 Gatewood Road, NE

department: Genomics Core

institute: Yerkes National Primate research center

description: Sample 24

data_processing:
All  mRNA-Seq samples were pooled and sequenced on NextSeq 500 using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing. The samples have 24 to 45 million pass filter reads with more than 94% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR. The average mapping rate of all samples is 97%. Unique alignment is above 83%. There are 1.79 to 3.80% unmapped reads. The mapping statistics are calculated using Picard software. The samples have 0.50% ribosomal bases. Percent coding bases are between 47-58%. Percent UTR bases are 28-37%, and mRNA bases are between 79-91% for all the samples. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have 67-81% non-duplicate reads. In addition, the gene expression quantification analysis was performed for all samples using STAR/RSEM tools. Both the normalized count and the raw count are provided as part of the data delivery
Genome_build: Human - hg38
Supplementary_files_format_and_content: Text files generated using RSEM v1.3.0  containing raw counts and FPKM values.

source_name: Peripheral mononuclear blood cells (PBMCs)

growth_protocol: [Cell culture protocol]  In order to maintain consistency and reduce potential batch effects RPMI was prepared from powder (US Biologicals). Fresh L-glutamine (Gibco) and dialyzed FBS (Thermo Fisher Scientific) were added immediately prior to use at a final concentration of 2 mM and 10% by volume respectively. HPLM was prepared as previously described (Cantor et al., 2017) along with four additional compounds: Uridine (3 µM), α-ketoglutarate (5 µM), acetylcarnitine (5 µM) and malate (5 µM). HPLM was supplemented with 10% dialyzed FBS throughout this study. HPLM-Min was prepared as HPLM for concentrations of ions, glucose and amino acids but polar metabolites were omitted (see Supplemental Table 1). RPMI was supplemented with 10% of either dialyzed (RPMIdFBS) or traditional FBS (RPMIcFBS). For long-term T cell proliferation assays, human recombinant IL-2 (Roche) was also added fresh immediately prior to use at a final concentration of 100 IU/ml. X-VIVO 15 media (Lonza) was used without additional serum. AIM-V media was a mixture of 50% RPMI and 50% AIM-V (Gibco) supplemented with 5% Normal Human Serum (Valley Biomedical). RPMI-Metabolites was prepared by adding the 31 small metabolites present in HPLM to basal RPMI and then supplementing with dialyzed FBS.

extract_protocol:
Peripheral blood mononuclear cells were freshly isolated from blood from healthy human donors of both sexes ranging from 25-60 years old. Naïve T cells were enriched via a negative selection kit (Miltenyi Biotech, 130-097-095) and either used immediately or stored in liquid nitrogen in a 9:1 mixture of FBS: dimethyl sulfoxide. For short-term activation assays, 96 well Nunc Maxisorp plates were coated with 1 to 10 ug/ml of anti-CD3/anti-CD28 antibodies in PBS for 2 to 4 hours at 37°C. Plates were then washed twice with PBS and enriched naïve T cells were added in the indicated media formulations. Levels of activation markers were measured by flow cytometry 16 to 24 hours later. For proliferation assays, cells were stained with Celltrace Violet and then activated as above. After three days, cells were transferred to a new plate with fresh media and analyzed by flow cytometry after another two days.
We used 100 ng – 1 ug of total RNA as the input to an mRNA capture with oligo-dT coated magnetic beads using Illumina TruSeq protocol. The mRNA is fragmented, and then a random-primed cDNA synthesis is performed. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification and then quantitated by qPCR followed by cluster generation and sequencing

treatment_protocol: Human T lymphocytes were activated and expanded in IL-2-containing media as described above for 15 to 20 days. The night before the assay, cells were placed in fresh media (either HPLM or RPMI) containing IL-2, and the following day were restimulated with either 1 mg/ml each of anti-CD3 (HIT3a, Biolegend) or PMA and ionomycin (Biolegend) for 6 or 5 hours respectively. Four hours prior to analysis, Brefeldin A was added (Biolegend). Following the restimulation, cells were washed in PBS, placed on ice and stained according to the protocol described above.

tag: age

value: Unknown

tag: Sex

value: Blood

tag: cell type

value: T lymphocytes

tag: cultured in

value: RPMI

tag: stimulated with

value: anti-CD3 and anti-CD28 antibodies

tag: time


title: T lymphocytes, Sample22_RPMI_Day5

description: Sample 22


title: T lymphocytes, Sample23_RPMI_Day5

description: Sample 23


title: T lymphocytes, Sample19_HPLM_Day5

description: Sample 19

value: HPLM


title: T lymphocytes, Sample18_RPMI_Day2

description: Sample 18


title: T lymphocytes, Sample21_HPLM_Day5

description: Sample 21


title: T lymphocytes, Sample17_RPMI_Day2

description: Sample 17


title: T lymphocytes, Sample16_RPMI_Day2

description: Sample 16


title: T lymphocytes, Sample20_HPLM_Day5

description: Sample 20


title: T lymphocytes, Sample15_HPLM_Day2

description: Sample 15


title: T lymphocytes, Sample14_HPLM_Day2

description: Sample 14


title: Breast cancer sample6

city: Nanjing

first: Yining

last: Yang

state: Jiangsu

address: 42 Baiziting Road

department: Clinical Laboratory

institute: Jiangsu Cancer Hospital

description:
Trimmed_Reads_Data: 13_cutadapt_trimmed.fa.gz
Aligned_Results: 13_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 13_human_novoalign_alignment_tRNA_raw.txt.gz

data_processing:
Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3’-aminoacyl (charged) deacylation to 3’-OH for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription.
Then pretreated total RNA was used to prepare the sequencing library in the following steps: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 135~160bp PCR amplified fragments (corresponding to 15~40nt small RNA size range).
The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as sequencing clusters and sequenced for 50 cycles on Illumina NextSeq500 system per the manufacturer’s instructions.
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter, trimmed 3’-adaptor bases by cut adapt) were aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb using NovoAlign software (v2.07.11).
The expression profiling and differential expression oftRFs&tiRNAs& known miRNAswere calculated based on normalized TPM.
Genome_build: hg19
Supplementary_files_format_and_content: The ExpresstDR.xlsx list shows tRF&tiRNA expression profiles.The tRF&tiRNA expression levels were measured and normalized as tag counts per million of total aligned tRNA reads (TPM). For each tRNA sequence-based profile, the number of tRNA sequence reads can be used to estimate expression level of each tRF&tiRNA.
Supplementary_files_format_and_content: The ComparetDR.xlsx list shows that when comparing two groups of profile differences (such as disease versus control) use the normalized tag number of tRNAs annotated in GtRNAdb, including the tag count of each sample, the “fold change” (i.e. the ratio of the group averages) between the groups for each tRF/tiRNA is computed.

source_name: mammary gland

growth_protocol: The samples were frozen freshly in liquid nitrogen and stored in -80 degrees Celsius until the specimens were used.

extract_protocol:
Total RNA was first pretreated  to remove some RNA modifications that interfere with small RNA-seq library construction by rtStar™ tRF&tiRNA Pretreatment Kit (Cat# AS-FS-005, Arraystar, MD, USA).
Diluted libraries were loaded onto reagent cartridge and forwarded to sequencing run on Illumina NextSeq 500 system using NextSeq 500 V2 kit (#FC-404-2005, Illumina, California, USA), according to the manufacturer’s instructions.

value: breast

tag: tumor stage

tag: state of organism

value: Initial diagnosis with no treatment

tag: molecule subtype

value: tRFs&tiRNAs


title: Adjacent normal sample4

description:
Trimmed_Reads_Data: 10_cutadapt_trimmed.fa.gz
Aligned_Results: 10_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 10_human_novoalign_alignment_tRNA_raw.txt.gz

value: normal sample


title: Adjacent normal sample6

description:
Trimmed_Reads_Data: 14_cutadapt_trimmed.fa.gz
Aligned_Results: 14_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 14_human_novoalign_alignment_tRNA_raw.txt.gz


title: Adjacent normal sample3

description:
Trimmed_Reads_Data: 8_cutadapt_trimmed.fa.gz
Aligned_Results: 8_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 8_human_novoalign_alignment_tRNA_raw.txt.gz


title: SacCer.RepTiming.15min.Replicate1a

tag: genotype

value: MATa ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 bar1::hisG ars608{delta}::HIS3 ars609{delta}::TRP1 ars305::TRP1 GPD-HSV-TK ADH1-hENT1 BrdU-Inc


title: T lymphocytes, Sample13_HPLM_Day2

description: Sample 13


title: Breast cancer sample4

description:
Trimmed_Reads_Data: 9_cutadapt_trimmed.fa.gz
Aligned_Results: 9_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 9_human_novoalign_alignment_tRNA_raw.txt.gz


title: Breast cancer sample3

description:
Trimmed_Reads_Data: 7_cutadapt_trimmed.fa.gz
Aligned_Results: 7_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 7_human_novoalign_alignment_tRNA_raw.txt.gz

value: malignant tumour


title: Breast cancer sample5

description:
Trimmed_Reads_Data: 11_cutadapt_trimmed.fa.gz
Aligned_Results: 11_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 11_human_novoalign_alignment_tRNA_raw.txt.gz


title: Control rep2

value: Sciatic nerves

value: Lewis

tag: gender

value: female

tag: group

value: Control


title: Adjacent normal sample2

description:
Trimmed_Reads_Data: 6_cutadapt_trimmed.fa.gz
Aligned_Results: 6_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 6_human_novoalign_alignment_tRNA_raw.txt.gz


title: Adjacent normal sample5

description:
Trimmed_Reads_Data: 12_cutadapt_trimmed.fa.gz
Aligned_Results: 12_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 12_human_novoalign_alignment_tRNA_raw.txt.gz


title: Adjacent normal sample1

description:
Trimmed_Reads_Data: 4_cutadapt_trimmed.fa.gz
Aligned_Results: 4_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 4_human_novoalign_alignment_tRNA_raw.txt.gz


title: Breast cancer sample2

description:
Trimmed_Reads_Data: 5_cutadapt_trimmed.fa.gz
Aligned_Results: 5_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 5_human_novoalign_alignment_tRNA_raw.txt.gz


title: Breast cancer sample1

description:
Trimmed_Reads_Data: 3_cutadapt_trimmed.fa.gz
Aligned_Results: 3_human_novoalign_alignment_tRNA.txt.gz
Detailed_Alignment_Information: 3_human_novoalign_alignment_tRNA_raw.txt.gz


title: Proseq_293T_D2G8-MED26-MUT_Rep2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Library strategy: PRO-Seq
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
Reads were then mapped to human genome hg38, with STAR aligner (version 2.5.3a) default settings, using Ensembl 87 annotation gene models.
Transcripts per kilobase millon (TPM) values were then generated using RSEM (version 1.3.0) function rsem-calculate-expression with option –estimate-rspd.
ChIP-seq reads were aligned to human genome hg38 using Bowtie2 (version 2.2.4) with default settings. Peaks were called using MACS2 callpeak (version 2.1.1), default parameter, based on the corresponding input samples. The peaks with qsocre < 1e-4 were then used for downstream analysis.
Bigwig files are normalized by the total reads of the spike-in genome and extended to fragment length for IP samples
Genome_build: UCSC genome hg38, ensembl 87 gene model
Supplementary_files_format_and_content: RNA-seq TPM in csv file, ChIP-seq in bigwig files

molecule: nuclear RNA

growth_protocol: Cells were cultured in 1X DMEM (Sigma-Aldrich) supplemented with 10% fetal bovine serum (Sigma-Aldrich), 1X Glutamine (ThermoFisher) and 1X penicillin/streptomycin (ThermoFisher) in a CO2 incubator (5% CO2) at 37°C.

extract_protocol:
For RNA-seq, total RNA was extracted using miRNeasy Mini Kit (Qiagen #217004) and quantified using RNA 6000 Nano Kit (Agilent Technologies) in Bioanalyzer. 1µg of total RNA was subjected to oligo-dT selection or removal of rRNA (Ribo-Zero rRNA removal kit ,Illumina, #MRZH11124). ERCC spike-ins from Ambion were added to RNA prior to library preparation.
For MED26 ChIP-seq, cells were crosslinked  with 2 mM DSG in PBS for 30 min and then 1% formaldehyde for 20 min. For Pol II ChIP-seq, human cells and mouse cells used for spike-in control were crosslinked with 1% formaldehyde for 20 min at room temperature. Human and mouse chromatin  were mixed in 10:1 ratio.  Crosslinked chromatin was sonicated to generate  fragments of 150-500 bp prior to immunoprecipitation.
For PRO-seq, around 25 million wild type or mutant HEK293T cells were mixed Drosophila Kc167 (10:1 ratio), permeabilised, and incubated with biotin-labeled NTPs. Biotinylated RNA was hydrolyzed with NaOH, and biotin containing RNA fragments were enriched by affinity purification using streptavidin-coated magnetic beads. A 3' sequencing adaptor was ligated to the biotinylated RNA, the 5'cap was removed,  5'OH was generated by base hydrolysis and converted to 5′ phosphate by treatment with T4 polynucleotide kinase, a 5′ sequencing adaptor was ligated to RNA. RNA was purified to enrich for biotinylated fragments with adaptor at both ends and reverse transcribed. Detailed methods are in PRO-Seq, Mahat et al Nat Protoc, 11:1455-76;  doi: 10.1038/nprot.2016.086.
Ribo-depleted RNA seq libraries were prepared using TruSeq Stranded Total RNA kit (Illumina, #20020596) following manufacturer's instructions. PolyA-selected RNA-seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina, #20020594) following manufacturer's instructions. Both TruSeq kits add Illumina-compatible adapter and indexes for sequencing.  Libraries were checked for quality (Bioanalyzer) and quantity (Qubit). Equimolar concentrations of libraries were pooled, requantified and sequenced as 50bp single reads on the Illumina HiSeq 2500 instrument. ChIP-seq libraries were prepared using KAPA HTP kit (Roche, #KK8234) and stock adapters by Bioo Scientific NEXTflex DNA barcodes with 15 cycles of PCR. Libraries were purified using Agencourt AMPure XP system and quantified using Bioanalyzer and Qubit fluorometer. Post amplification size selection was performed on all libraries using Pippin-prep (Sage Science) instument. Equimolar concentrations of libraries were pooled, requantified and sequenced either as single reads on the Illumina HiSeq 2500 platform (polyA-selected RNA-seq and MED26 ChIP-seq) or as single read High Output on Illumina NextSeq 500 platform (ribo-depleted RNA-seq and Pol II ChIP-seq). PRO-seq libraries were generated essentially as described in Mahat et al., 2016 (Nat Protoc, 11:1455-76;  doi: 10.1038/nprot.2016.086). Primers RPI4, RPI5, RPI6 and RPI7 were used to barcode cDNAs from 293T_WT_Rep1 (Wild Type, replicate 1), 293T_WT_Rep2 (Wild Type, replicate 2), 293_D2G8-MED26-MUT_Rep1 (Mutant MED26-D2G8, replicate 1), and 293_D2G8-MED26-MUT_Rep2 (Mutant MED26-D2G8, replicate 2) respectively.

treatment_protocol: siRNAs specific for human MED26, AFF4, ICE1 and Non-target were purchased from Dharmacon (SMARTpool) or ThermoFisher (Silencer Select).

tag: chromatin spike-in organism

value: Drosophila melanogaster

tag: protocol

value: PRO-Seq, Mahat et al Nat Protoc, 11:1455-76;  doi:10.1038/nprot.2016.086


title: Proseq_293T_WT_Rep1


title: Proseq_293T_D2G8-MED26-MUT_Rep1


title: Proseq_293T_WT_Rep2


title: 293T-D2G8-MED26-MUT_Rpb1-IP_Rep1

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
Reads were then mapped to human genome hg38, with STAR aligner (version 2.5.3a) default settings, using Ensembl 87 annotation gene models.
Transcripts per kilobase millon (TPM) values were then generated using RSEM (version 1.3.0) function rsem-calculate-expression with option –estimate-rspd.
ChIP-seq reads were aligned to human genome hg38 using Bowtie2 (version 2.2.4) with default settings. Peaks were called using MACS2 callpeak (version 2.1.1), default parameter, based on the corresponding input samples. The peaks with qsocre < 1e-4 were then used for downstream analysis.
Bigwig files are normalized by the total reads of the spike-in genome and extended to fragment length for IP samples
Genome_build: UCSC genome hg38, ensembl 87 gene model
Supplementary_files_format_and_content: RNA-seq TPM in csv file, ChIP-seq in bigwig files

value: Mus Musculus

tag: chip antibody

value: anti-Rpb1 D8L4Y, Cell Signaling cat 14958S


title: 293T-WT_Rpb1_Input_Rep1

value: none (input)


title: 293T-WT_Rpb1_Input_Rep2


title: 293T-D2G8-MED26-MUT_Rpb1-IP_Rep2


title: 293T-D2G8-MED26-MUT_Rpb1_Input_Rep2


title: 293T-WT_Rpb1_IP_Rep2


title: 293T-D2G8-MED26-MUT_Rpb1_Input_Rep1


title: 293T-WT_Rpb1_IP_Rep1


title: NKT.Sp.18hLPS.165ugNo2

first: Edy

middle: Yong

last: Kim

address: 60 Fenwood Rd

institute: Brigham and Women’s Hospital

data_processing:
Reads were mapped to the mouse reference genome (mm10) with HISAT 0.1.6-beta
Bam files were sorted and indexed by SAMtools 1.2
Assembly, quantification and normalization were performed using CuffLinks 1.2, according to the Tuxedo pipeline
A merged transcriptome constructed from all samples of all data sets was used as a reference annotation for quantification (by CuffQuant) and normalization (by CuffNorm)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Splenic NKT

growth_protocol: 10 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

treatment_protocol: Some organisms were treated with 50ug or 165ug ultra-pure LPS after 3h, 18h or 3 days.

tag: strain

value: 10 weeks old

tag: treatment

value: 165ug LPS

value: wild type

tag: tissue

value: Spleen

value: Splenic NKT


title: Tgd.Sp.3hLPS.50ugNo2

source_name: Splenic Tgd

tag: age

value: 50ug LPS

value: Splenic Tgd


title: NKT.Sp.d3LPS.50ugNo2

tag: cell type


title: Tgd.SpNo2

value: 0ug LPS


title: NKT.Sp.3hLPS.165ugNo1


title: NK.SpNo2

source_name: Splenic NK

value: Splenic NK


title: NK.SpNo1


title: Tgd.Sp.3hLPS.165ugNo1


title: Tgd.Sp.18hLPS.165ugNo1


title: NKT.Sp.18hLPS.50ugNo2


title: NKT.Sp.18hLPS.50ugNo1


title: NKT.Sp.18hLPS.165ugNo1


title: NKT.Sp.3hLPS.50ugNo2


title: NKT.SpNo1


title: Tgd.Sp.3hLPS.165ugNo2


title: Tgd.Sp.d3LPS.165ugNo1


title: NKT.Sp.3hLPS.50ugNo1


title: NKT.SpNo2


title: NKT.Sp.d3LPS.165ugNo1


title: Tgd.Sp.d3LPS.165ugNo2


title: Tgd.Sp.3hLPS.50ugNo1


title: Tgd.Sp.18hLPS.50ugNo2


title: NKT.Sp.d3LPS.165ugNo2


title: Tgd.SpNo1


title: Tgd.Sp.18hLPS.165ugNo2


title: Tgd.Sp.18hLPS.50ugNo1


title: NKT.Sp.3hLPS.165ugNo2


title: NK.Sp.d3LPS.165ugNo2


title: NKT.Sp.d3LPS.50ugNo1


title: NK.Sp.d3LPS.165ugNo1


title: NK.Sp.3hLPS.165ugNo1


title: NK.Sp.18hLPS.165ugNo2


title: HDAC_ChIP_4

city: Austin

first: Steven

last: Vokes

address: 2500 Speedway, Stop A4800

department: Department of Molecular Biosciences, Institute for Cellular & Molecular Biology

institute: The University of Texas at Austin

data_processing:
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using CisGenome with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files: peaks called by CisGenome

source_name: 3 litters FL+ HL

extract_protocol:
Limb buds were dissected and limbs were dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes.
ChIP libraries were prepared with NEBNext Ultra II Library Prep Kit or Diagenode MicroPlex Library Prep, with 15 cycles of library amplifications. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.

tag: strain/background

value: Swiss Webster

value: forelimb and hindlimb buds

tag: Stage

value: HDAC1 antibody (Abcam ab7028)


title: HDAC_input_4


title: NK.Sp.18hLPS.165ugNo1

tag: time


title: MF.6Cplus.SpNo1

source_name: Splenic Ly6c+ macrophages

value: Splenic Ly6c+ macrophages


title: MF.6Cplus.Sp.18hLPS.165ugNo2


title: MF.6C_SpNo1

source_name: Splenic Ly6c- macrophages

value: Splenic Ly6c- macrophages


title: MF.6C_SpNo2


title: MF.6Cplus.Sp.18hLPS.165ugNo1


title: NK.Sp.3hLPS.165ugNo2


title: MF.6Cplus.Sp.d3LPS.165ugNo1


title: NK.Sp.18hLPS.50ugNo1


title: MF.6Cplus.SpNo2


title: MF.6Cplus.Sp.3hLPS.165ugNo1


title: MF.6Cplus.Sp.d3LPS.165ugNo2


title: MF.6Cplus.Sp.18hLPS.50ugNo2


title: MF.6C_Sp.18hLPS.50ugNo1


title: MF.6C_Sp.18hLPS.165ugNo1


title: HDAC_input_3


title: MF.6Cplus.Sp.3hLPS.165ugNo2


title: NK.Sp.18hLPS.50ugNo2


title: MF.6C_Sp.d3LPS.165ugNo2


title: MF.6C_Sp.3hLPS.165ugNo1


title: MF.6Cplus.Sp.18hLPS.50ugNo1


title: MF.6C_Sp.18hLPS.50ugNo2


title: HDAC_ChIP_3


title: MF.6C_Sp.d3LPS.165ugNo1


title: MF.6C_Sp.3hLPS.165ugNo2


title: MF.6C_Sp.18hLPS.165ugNo2


title: HDAC_input


title: FBXL19fl_ES_RA72hrs_rep2_ATACseq

city: Oxford

first: Angelika

last: Feldmann

state: England

address: South Parks Road

country: United Kingdom

institute: University of Oxford, Department of Biochemistry

data_processing:
Reads were aligned to mm10 genome using Bowtie 2 with the ‘-- no-mixed’ and ‘-- no-discordant’ options (Langmead and Salzberg 2012). Reads that were mapped more than once were discarded, PCR duplicates were removed using SAMTools (Li et al. 2009). Reads that mapped to a custom ‘blacklist’ of genomic regions with artificially high counts, including mitochondrial DNA sequences, were also discarded.
For data visualisation, mm10 reads were randomly subsampled by a factor that reflects the total number of reads in the same sample, as previously described (Bonhoure et al. 2014; Orlando et al. 2014; Hu et al. 2015).
For each condition, downsampled biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
ATAC-seq enrichments were quantified from BAM files using the summarizeOverlaps() function from GenomicFeatures. Log2 transformations were calculated following the addition of a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for raw and merged replicates of normalised ChIP-seq

source_name: Mouse embryonic stem cells, control, retinoic-acid treated (72hr RA), ATAC-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor.

extract_protocol:
Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al. 2013) as previously described (King and Klose 2017), using 5x10^5 nuclei.
ATAC-seq libraries were prepared by PCR amplification using custom-made Illumina barcodes (Buenrostro et al. 2013) and the NEBNext High-Fidelity 2X PCR Master Mix (NEB). Libraries were purified with two rounds of Agencourt AMPure XP bead cleanup (Agencourt, 1.5X bead:sample ratio), and were sequenced using the Illumina NextSeq 500 platform in biological quadruplicate using 75 bp paired-end reads.

treatment_protocol: To induce RA-differentiation mouse ES cells were treated with 1uM retinoic acid (RA)

tag: cell line

value: E14 mouse embryonic stem cells

tag: replicate

tag: treatment agent

value: retinoic acid (RA)

tag: treatment time point

value: 72 hr


title: FBXL19fl_ES_UNT_rep4_ATACseq

source_name: Mouse embryonic stem cells, untreated control, ATAC-seq

value: 0 hr


title: FBXL19fl_ES_UNT_rep3_ATACseq


title: FBXL19fl_ES_UNT_rep2_ATACseq


title: FBXL19fl_ES_RA72hrs_rep1_ATACseq


title: FBXL19fl_ES_RA72hrs_rep3_ATACseq


title: FBXL19fl_ES_RA72hrs_rep3_NatInput

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6 for native cChIP-seq and mm10+hg19 for cross-linked cChIP-seq) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools for native cChIP-seq or Sambamba for cross-linked cChIP-seq.
For annotation of genomic intervals and data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of reads in each sample.
For each condition, downsampled biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
ChIP-seq enrichments were quantified from BAM files using the summarizeOverlaps() function from GenomicFeatures. Log2 transformations were calculated following the addition of a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for raw and merged replicates of normalised ChIP-seq

source_name: Mouse embryonic stem cells, control, retinoic-acid treated (72hr RA), H3K4me1 gDNA-Seq

extract_protocol:
For native ChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following RA treatment) were collected and washed once in PBS. Cells were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 10 mM N-ethylmaleimide, 1x protease inhibitors (Sigma)). Each sample was then incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitors, 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes.
Libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7103), following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on Illumina NextSeq 500 platform in biological quadruplicate.

tag: ChIP

tag: antibody


title: FBXL19fl_ES_RA72hrs_rep4_ATACseq


title: FBXL19fl_ES_RA72hrs_rep2_ChIP_H3K4me1

source_name: Mouse embryonic stem cells, control, retinoic-acid treated (72hr RA), H3K4me1 ChIP-Seq

value: Cell Signaling Technology(#5326 )


title: FBXL19fl_ES_UNT_rep1_NatInput

source_name: Mouse embryonic stem cells, untreated control, H3K4me1 gDNA-Seq


title: FBXL19fl_ES_UNT_rep2_NatInput


title: FBXL19fl_ES_UNT_rep1_ChIP_H3K4me1

source_name: Mouse embryonic stem cells, untreated control, H3K4me1 ChIP-Seq


title: FBXL19fl_ES_UNT_rep3_NatInput


title: FBXL19fl_ES_UNT_rep1_ATACseq


title: FBXL19fl_ES_UNT_rep3_ChIP_H3K4me1


title: FBXL19fl_ES_RA72hrs_rep1_ChIP_H3K4me1


title: FBXL19fl_ES_UNT_rep4_ChIP_H3K4me1


title: FBXL19fl_ES_RA72hrs_rep3_ChIP_H3K4me1


title: FBXL19fl_ES_RA72hrs_rep4_ChIP_H3K4me1


title: FBXL19fl_ES_UNT_rep2_ChIP_H3K4me1


title: FBXL19fl_ES_UNT_rep4_NatInput


title: Meninges ILC2

city: Albany

first: Ivan Ting Hin

last: Fung

state: NY

address: 47 New Scotland Ave

institute: Albany Medical College

description: 7x 400ng IL-33 IP

data_processing:
Library was generated using chromium 5' gene expression kit (10Xgenomincs).
Reference genome mouse (mm10) was used for read alignment and gene expression quantification using Cellranger v3.1.0 pipelines.
The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines.
These pipelines combine Chromium specific algorithms with the RNA-seq aligner STAR.
Genome_build: mm10
Supplementary_files_format_and_content: mtx and tsv for processed data, bam for each sample

source_name: Sorted ILC2 from the Meninges

extract_protocol:
ILC2 from the choroid plexus and meninges were sorted based on their surface marker expressions. Total RNA extracted following the instructions of the 10X genomics kit
scRNA-seq libraries were prepared using the 5’ single cell gene expression kit  (10x Genomics) accoding to the manufacturer’s instruction

treatment_protocol: Aged mice (20-22mos) were injected with 400ng of IL-33 daily for 7 days.

value: Meninges

value: Sorted ILC2


title: MED13-13lfl_ES_TAM_rep3_CapC_set2

description:
processed data file:
Fli1_id3186524_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mn1_id1964984_MED13_ES_TAM_bg.bed_bg_sorted.bw
Kif26b_id440003_MED13_ES_TAM_bg.bed_bg_sorted.bw
Dlk1_id4283906_MED13_ES_TAM_bg.bed_bg_sorted.bw
Spry1_id1010657_MED13_ES_TAM_bg.bed_bg_sorted.bw
Igdcc3_id3267532_MED13_ES_TAM_bg.bed_bg_sorted.bw
Col26a1_id2027715_MED13_ES_TAM_bg.bed_bg_sorted.bw
Samd14_id3955395_MED13_ES_TAM_bg.bed_bg_sorted.bw
Atoh8_id2237664_MED13_ES_TAM_bg.bed_bg_sorted.bw

data_processing:
library strategy: CaptureC
For CaptureC, paired-end reads were aligned and filtered for HiC artefacts using HiCUP (Wingett S, et al. (2015)) and Bowtie2 (Langmead and Salzberg, 2012) with fragment filter set to 100-800bp. Read counts of reads aligning to captured gene promoters and interaction scores (=significant interactions) were then called  by CHiCAGO (Cairns et al., 2016).
For visualisation of CaptureC data weighted pooled read counts from chicago data files were normalized to total read count aligning to captured gene promoters in the sample and further to the number of promoters in the respective capture experiment. Bigwig files were generated from these normalized read counts.
For comparative boxplot analysis interactions called by chicago (score >= 5) across all samples were aggregated and interactions with a distance of less than 4 DpnII fragments were merged to a single interaction peak. For each interaction peak we then quantified mean normalized read count and chicago score of all overlapping DpnII fragments.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files showing the genome coverage of normalized read counts for each sample and each promoter were generated from chicago data object.

source_name: mESCs_tamoxifen-treated (96hr OHT), CaptureC

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. Human HEK293T cells used for calibrated ChIP-seq were grown at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), and 0.5 mM beta-mercaptoethanol (Life Technologies). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
CaptureC libraries were prepared as described previously (Hughes et al., Nature Genetics 2014). Briefly, 10 Million mouse ES cells were trypsinized, collected in 50ml falcon tubes in 9.3ml media and crosslinked with 1.25ml 16% formaldehyde for 10min at room temperature. Cells were quenched with 1.5M glycine, washed with PBS and lysed for 20 minutes at 4oC lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40, supplemented with complete proteinase inhibitors) prior to snap freezing in 1ml lysis buffer at -80oC.
Lysates were then thawed on ice, pelleted and resuspended in 650µl 1x DpnII buffer (NEB). Three 1.5ml tubes with 200µl lysate each were treated in parallel with SDS (0.28% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off), quenched with trypsin (1.67% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off) and subjected to a 24 hour digestion with 3x10µl DpnII (homemade, 37 oC, interval shaking 500rpm, 30sec on/30sec off). Each chromatin aliquot was independently ligated with 8 µl T4 Ligase (240 U) in a volume of 1440µl (20 hours, 16oC). Following this, the nuclei containing ligated chromatin were pelleted to remove any non-nuclear chromatin, reverse-crosslinked and the ligated DNA was phenol-chloroform purified. The sample was resupended in 300µl water and sonicated 13x (Pico Bioruptor, 30sec on, 30sec off) or until a fragment size of approximately 200bp was reached. Fragments were size selected using AmpureX beads (Beckman Coulter: A63881, selection ratios: 0.85x / 0.4x). 2x 1-5µg of DNA were adaptor ligated and indexed using the NEBNext DNA library Prep Reagent Set (New England Biolabs: E6040S/L) and NEBNext Multiplex Oligos for Illumina Primer sets 1 (New England: E7335S/L) and 2 (New England: E7500S/L). The libraries were amplified 7x using Herculase II Fusion Polymerase kit (Agilent: 600677). Libraries were hybridized in teh following way: Probes were designed using the online tool by the Hughes lab (CapSequm: http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) to be either 120bp (Sox2) or 70bp long each, two probes for each promoter of interest. The probes were pooled at a 2.9nM each and the samples were multiplexed by mass prior to hybridization. Hybridization was carried out using the Nimblegen SeqCap system (Roche, Nimblegen SeqCap EZ HE-oligo kit A # 06777287001, Nimblegen SeqCap EZ HE-oligo kit B # 06777317001, Nimblegen SeqCap EZ Accessory kit v2 # 07145594001, Nimblegen SeqCap EZ Hybridisation and wash kit # 05634261001) according to Roche protocol for 72 hours followed by a 24 hours hybridization (double Capture). The captured libraries were sequenced on Illumina NextSeq.

treatment_protocol: To induce conditional removal of the Fbxl19 CxxC domain or Med13 and Med13l in FBXL19fl and MED13/13lfl ESC lines, cells were treated with 800nM 4-hydroxytamoxifen (TAM) for 96 hours. To induce differentiation, ES cells were treated with 1uM retinoic acid (RA) for 72 hours.

value: Mouse embryonic stem cells

tag: cell line background

tag: genotype

value: Med13/13lfl/fl; Rosa26::ERT2-Cre

value: tamoxifen (OHT)

value: 96 hr


title: HDAC_ChIP_1

tag: chip antibody


title: FBXL19fl_ES_RA72hrs_rep1_NatInput


title: FBXL19fl_ES_RA72hrs_rep2_NatInput


title: FBXL19fl_ES_RA72hrs_rep4_NatInput


title: CP ILC2

description: 7x 400ng IL-33 IP

source_name: Sorted ILC2 from the Choroid Plexus

tag: strain

value: injected with 400ng of IL-33 daily for 7 days

value: Choroid Plexus


title: MED13-13lfl_ES_TAM_rep2_CapC_set2


title: MED13-13lfl_ES_TAM_rep1_CapC_set2


title: MED13-13lfl_ES_UNT_rep2_CapC_set2

description:
processed data file:
Fli1_id3186524_MED13_ES_UNT_bg.bed_bg_sorted.bw
Mn1_id1964984_MED13_ES_UNT_bg.bed_bg_sorted.bw
Kif26b_id440003_MED13_ES_UNT_bg.bed_bg_sorted.bw
Dlk1_id4283906_MED13_ES_UNT_bg.bed_bg_sorted.bw
Spry1_id1010657_MED13_ES_UNT_bg.bed_bg_sorted.bw
Igdcc3_id3267532_MED13_ES_UNT_bg.bed_bg_sorted.bw
Col26a1_id2027715_MED13_ES_UNT_bg.bed_bg_sorted.bw
Samd14_id3955395_MED13_ES_UNT_bg.bed_bg_sorted.bw
Atoh8_id2237664_MED13_ES_UNT_bg.bed_bg_sorted.bw

source_name: mESCs_untreated control, CaptureC


title: MED13-13lfl_ES_UNT_rep3_CapC_set2


title: MED13-13lfl_ES_TAM_rep2_CapC_set1

description:
processed data file:
Tpm4_id2969160_MED13_ES_TAM_bg.bed_bg_sorted.bw
Megf10_id5749717_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ckap2_id2847141_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ccdc177_id4213506_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ankrd6_id1387983_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pdp2_id3050157_MED13_ES_TAM_bg.bed_bg_sorted.bw
Kdm7a_id2153561_MED13_ES_TAM_bg.bed_bg_sorted.bw
AW146154_id2537634_MED13_ES_TAM_bg.bed_bg_sorted.bw
Slc47a2_id3871357_MED13_ES_TAM_bg.bed_bg_sorted.bw
Asic2_id3923197_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tmco1_id411517_MED13_ES_TAM_bg.bed_bg_sorted.bw
Evi5l_id2802851_MED13_ES_TAM_bg.bed_bg_sorted.bw
Arrdc3_id4506220_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cep126_id3124148_MED13_ES_TAM_bg.bed_bg_sorted.bw
C77370_id6243560_MED13_ES_TAM_bg.bed_bg_sorted.bw
Lonrf1_id2881524_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ermp1_id5897272_MED13_ES_TAM_bg.bed_bg_sorted.bw
Polr3a_id4659089_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ccdc142_id2265006_MED13_ES_TAM_bg.bed_bg_sorted.bw
Stat5b_id3969874_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tiam2_id5387471_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ednrb_id4854605_MED13_ES_TAM_bg.bed_bg_sorted.bw
Syce1_id2788219_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ppfia4_id331310_MED13_ES_TAM_bg.bed_bg_sorted.bw
1500009L16Rik_id3612757_MED13_ES_TAM_bg.bed_bg_sorted.bw
Dnajc13_id3362998_MED13_ES_TAM_bg.bed_bg_sorted.bw
Adamtsl3_id2641148_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pak3_id6344953_MED13_ES_TAM_bg.bed_bg_sorted.bw
E030018B13Rik_id2596176_MED13_ES_TAM_bg.bed_bg_sorted.bw
Sema6d_id778751_MED13_ES_TAM_bg.bed_bg_sorted.bw
Inafm2_id765330_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cabp1_id1973991_MED13_ES_TAM_bg.bed_bg_sorted.bw
Prdx3_id5973264_MED13_ES_TAM_bg.bed_bg_sorted.bw
Aplp1_id2508467_MED13_ES_TAM_bg.bed_bg_sorted.bw
Arg1_id3465762_MED13_ES_TAM_bg.bed_bg_sorted.bw
Rhob_id4035130_MED13_ES_TAM_bg.bed_bg_sorted.bw
Casp2_id2161600_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cdh6_id4930340_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cnn2_id3603335_MED13_ES_TAM_bg.bed_bg_sorted.bw
Col8a1_id5290658_MED13_ES_TAM_bg.bed_bg_sorted.bw
Epha5_id1896100_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mpzl2_id3218449_MED13_ES_TAM_bg.bed_bg_sorted.bw
Fasn_id4018679_MED13_ES_TAM_bg.bed_bg_sorted.bw
Fzd7_id142589_MED13_ES_TAM_bg.bed_bg_sorted.bw
Fzd8_id5631876_MED13_ES_TAM_bg.bed_bg_sorted.bw
Gas1_id4452406_MED13_ES_TAM_bg.bed_bg_sorted.bw
Hoxb1_id3958722_MED13_ES_TAM_bg.bed_bg_sorted.bw
Hoxb5_id3958568_MED13_ES_TAM_bg.bed_bg_sorted.bw
Hpgd_id2929245_MED13_ES_TAM_bg.bed_bg_sorted.bw
Klf2_id2969645_MED13_ES_TAM_bg.bed_bg_sorted.bw
Lfng_id2036913_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mapkapk2_id323408_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mcm3_id47198_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mmp15_id3027407_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mmp2_id3020918_MED13_ES_TAM_bg.bed_bg_sorted.bw
Gadd45b_id3605594_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pla2r1_id622128_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ptprn_id180345_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ptrf_id3970218_MED13_ES_TAM_bg.bed_bg_sorted.bw
S100a10_id1149986_MED13_ES_TAM_bg.bed_bg_sorted.bw
Nkx1-2_id2768203_MED13_ES_TAM_bg.bed_bg_sorted.bw
Scd1_id5933791_MED13_ES_TAM_bg.bed_bg_sorted.bw
Supt4a_id3937444_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tal2_id1439711_MED13_ES_TAM_bg.bed_bg_sorted.bw
Hnf1a_id1973455_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ttf1_id545321_MED13_ES_TAM_bg.bed_bg_sorted.bw
Vipr2_id4301021_MED13_ES_TAM_bg.bed_bg_sorted.bw
Abcg1_id5455875_MED13_ES_TAM_bg.bed_bg_sorted.bw
Asic1_id5143940_MED13_ES_TAM_bg.bed_bg_sorted.bw
Capn2_id449358_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cd24a_id3512611_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cdh11_id3045509_MED13_ES_TAM_bg.bed_bg_sorted.bw
Chat,Slc18a3_id4678235_MED13_ES_TAM_bg.bed_bg_sorted.bw
S1pr3_id4431509_MED13_ES_TAM_bg.bed_bg_sorted.bw
Efs_id4735760_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ephb3_id5201786_MED13_ES_TAM_bg.bed_bg_sorted.bw
Fhl3_id1618914_MED13_ES_TAM_bg.bed_bg_sorted.bw
Gsto1_id5942000_MED13_ES_TAM_bg.bed_bg_sorted.bw
Hoxb3_id3958676_MED13_ES_TAM_bg.bed_bg_sorted.bw
Igfbp5_id174464_MED13_ES_TAM_bg.bed_bg_sorted.bw
Itga5_id5153214_MED13_ES_TAM_bg.bed_bg_sorted.bw
Lama3_id5639740_MED13_ES_TAM_bg.bed_bg_sorted.bw
Large_id2972265_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ndufa4_id2086878_MED13_ES_TAM_bg.bed_bg_sorted.bw
Nfkbia_id4151479_MED13_ES_TAM_bg.bed_bg_sorted.bw
Numbl_id2500220_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pou3f1_id1618825_MED13_ES_TAM_bg.bed_bg_sorted.bw
Prlr_id4923288_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pros1_id5303530_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ptprd_id1501257_MED13_ES_TAM_bg.bed_bg_sorted.bw
Scnn1g_id2741113_MED13_ES_TAM_bg.bed_bg_sorted.bw
St8sia1_id2413404_MED13_ES_TAM_bg.bed_bg_sorted.bw
Sox2_id1003349_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tcea3_id1647459_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tubb5_id5468158_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ercc5_id104061_MED13_ES_TAM_bg.bed_bg_sorted.bw
Amfr_id3024072_MED13_ES_TAM_bg.bed_bg_sorted.bw
C1ql1_id3975329_MED13_ES_TAM_bg.bed_bg_sorted.bw
Creg1_id407574_MED13_ES_TAM_bg.bed_bg_sorted.bw
Twf2_id3367775_MED13_ES_TAM_bg.bed_bg_sorted.bw
St6galnac5_id1294639_MED13_ES_TAM_bg.bed_bg_sorted.bw
Asns_id2075943_MED13_ES_TAM_bg.bed_bg_sorted.bw
Fkbp9_id2196958_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cpt1a_id5832120_MED13_ES_TAM_bg.bed_bg_sorted.bw
Frg1_id2894123_MED13_ES_TAM_bg.bed_bg_sorted.bw
Hebp1_id2394582_MED13_ES_TAM_bg.bed_bg_sorted.bw
Lrpap1_id1775334_MED13_ES_TAM_bg.bed_bg_sorted.bw
Atp5l_id3218128_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tnfrsf19_id4750989_MED13_ES_TAM_bg.bed_bg_sorted.bw
Scly_id220349_MED13_ES_TAM_bg.bed_bg_sorted.bw
Gipc2_id1292782_MED13_ES_TAM_bg.bed_bg_sorted.bw
Insm1_id832241_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ctnnal1_id1447659_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ntsr1_id917074_MED13_ES_TAM_bg.bed_bg_sorted.bw
Slc1a4_id3770078_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ppie_id1615141_MED13_ES_TAM_bg.bed_bg_sorted.bw
Htra1_id2764107_MED13_ES_TAM_bg.bed_bg_sorted.bw
Arl10_id4439192_MED13_ES_TAM_bg.bed_bg_sorted.bw
Angptl4_id5462755_MED13_ES_TAM_bg.bed_bg_sorted.bw
Egr4_id2270850_MED13_ES_TAM_bg.bed_bg_sorted.bw
Snrpb2_id824501_MED13_ES_TAM_bg.bed_bg_sorted.bw
Shank3_id5119599_MED13_ES_TAM_bg.bed_bg_sorted.bw
Isl1_id4592795_MED13_ES_TAM_bg.bed_bg_sorted.bw
Slc4a8_id5146726_MED13_ES_TAM_bg.bed_bg_sorted.bw
Foxj2_id2362399_MED13_ES_TAM_bg.bed_bg_sorted.bw
Paqr4_id5438307_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tbc1d20_id847836_MED13_ES_TAM_bg.bed_bg_sorted.bw
Rexo2_id3226797_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tomm7_id1746923_MED13_ES_TAM_bg.bed_bg_sorted.bw
Llph_id3700641_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tma16_id2954862_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mrps14_id394136_MED13_ES_TAM_bg.bed_bg_sorted.bw
Isoc1_id5753246_MED13_ES_TAM_bg.bed_bg_sorted.bw
Polr2e_id3603475_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mrps25_id2287411_MED13_ES_TAM_bg.bed_bg_sorted.bw
Sorcs3_id5942915_MED13_ES_TAM_bg.bed_bg_sorted.bw
Uqcrfs1_id4380171_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tril_id2189634_MED13_ES_TAM_bg.bed_bg_sorted.bw
Eef1g_id5846437_MED13_ES_TAM_bg.bed_bg_sorted.bw
Snrpd3_id3591800_MED13_ES_TAM_bg.bed_bg_sorted.bw
Map1lc3b_id3091625_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pkp2_id5188447_MED13_ES_TAM_bg.bed_bg_sorted.bw
Dph2_id1601224_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ufm1_id1050580_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tmem86a_id2552408_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mrpl19_id2261989_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cdc42ep3_id5577780_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ndufb4_id5241422_MED13_ES_TAM_bg.bed_bg_sorted.bw
1110007C09Rik_id4425616_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mocos_id5670125_MED13_ES_TAM_bg.bed_bg_sorted.bw
Dus1l_id4018609_MED13_ES_TAM_bg.bed_bg_sorted.bw
Slc52a3_id847064_MED13_ES_TAM_bg.bed_bg_sorted.bw
Rhpn2_id2522257_MED13_ES_TAM_bg.bed_bg_sorted.bw
Nkd2_id4487550_MED13_ES_TAM_bg.bed_bg_sorted.bw
Wdr89_id4201123_MED13_ES_TAM_bg.bed_bg_sorted.bw
Lrpprc_id5590892_MED13_ES_TAM_bg.bed_bg_sorted.bw
Phykpl_id3847043_MED13_ES_TAM_bg.bed_bg_sorted.bw
Zfp493_id4472135_MED13_ES_TAM_bg.bed_bg_sorted.bw
Ptchd4_id5486398_MED13_ES_TAM_bg.bed_bg_sorted.bw
Zbtb8a_id1630475_MED13_ES_TAM_bg.bed_bg_sorted.bw
Irak3_id3700588_MED13_ES_TAM_bg.bed_bg_sorted.bw
Zfp819_id2543728_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pck2_id4737370_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pcdh1_id5703772_MED13_ES_TAM_bg.bed_bg_sorted.bw
Fam101b_id3908213_MED13_ES_TAM_bg.bed_bg_sorted.bw
Sgpp1_id4201286_MED13_ES_TAM_bg.bed_bg_sorted.bw
Hspa8_id3208123_MED13_ES_TAM_bg.bed_bg_sorted.bw
Kcnn1_id2965914_MED13_ES_TAM_bg.bed_bg_sorted.bw
Spred2_id3769103_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tshz2_id890477_MED13_ES_TAM_bg.bed_bg_sorted.bw
Acss1_id843594_MED13_ES_TAM_bg.bed_bg_sorted.bw
Nphs2_id384824_MED13_ES_TAM_bg.bed_bg_sorted.bw
Arhgef5_id2164246_MED13_ES_TAM_bg.bed_bg_sorted.bw
Abhd17c_id2645639_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cdcp1_id3409272_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cisd1_id3581396_MED13_ES_TAM_bg.bed_bg_sorted.bw
Hoxb2_id3958685_MED13_ES_TAM_bg.bed_bg_sorted.bw
Smim3_id5757976_MED13_ES_TAM_bg.bed_bg_sorted.bw
Socs7_id3961207_MED13_ES_TAM_bg.bed_bg_sorted.bw
Nlgn1_id982921_MED13_ES_TAM_bg.bed_bg_sorted.bw
Susd4_id449923_MED13_ES_TAM_bg.bed_bg_sorted.bw
Zswim6_id4572766_MED13_ES_TAM_bg.bed_bg_sorted.bw
Zfp503_id4652828_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pim3_id5118011_MED13_ES_TAM_bg.bed_bg_sorted.bw
Lace1_id3510061_MED13_ES_TAM_bg.bed_bg_sorted.bw
Lrrc3b_id4635973_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cpped1_id5177046_MED13_ES_TAM_bg.bed_bg_sorted.bw
Aars_id3066336_MED13_ES_TAM_bg.bed_bg_sorted.bw
Prss50_id3379869_MED13_ES_TAM_bg.bed_bg_sorted.bw
Slc1a3_id4919615_MED13_ES_TAM_bg.bed_bg_sorted.bw
Rbm17_id500778_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cd109_id3300227_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cadm4_id2492585_MED13_ES_TAM_bg.bed_bg_sorted.bw
Gpr156_id5242053_MED13_ES_TAM_bg.bed_bg_sorted.bw
Cmtm4_id3049681_MED13_ES_TAM_bg.bed_bg_sorted.bw
Acsf2_id3954253_MED13_ES_TAM_bg.bed_bg_sorted.bw
Nfkbid_id2508402_MED13_ES_TAM_bg.bed_bg_sorted.bw
Oscp1_id1622319_MED13_ES_TAM_bg.bed_bg_sorted.bw
Rbm34_id3104231_MED13_ES_TAM_bg.bed_bg_sorted.bw
Sh3rf3_id3550886_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tbcel_id3212157_MED13_ES_TAM_bg.bed_bg_sorted.bw
Galnt18_id2716596_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mamdc2_id5882597_MED13_ES_TAM_bg.bed_bg_sorted.bw
Fbxl22_id3270912_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mael_id408645_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mroh1_id5086983_MED13_ES_TAM_bg.bed_bg_sorted.bw
Zfp770_id754414_MED13_ES_TAM_bg.bed_bg_sorted.bw
Prtg_id3286160_MED13_ES_TAM_bg.bed_bg_sorted.bw
Aard_id5025738_MED13_ES_TAM_bg.bed_bg_sorted.bw
Rab11fip4_id3917225_MED13_ES_TAM_bg.bed_bg_sorted.bw
Pld5_id434386_MED13_ES_TAM_bg.bed_bg_sorted.bw
Nwd2_id1845589_MED13_ES_TAM_bg.bed_bg_sorted.bw
Samd12_id5030415_MED13_ES_TAM_bg.bed_bg_sorted.bw
Arl4c_id214048_MED13_ES_TAM_bg.bed_bg_sorted.bw
Arap2_id1843354_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tagln2_id424572_MED13_ES_TAM_bg.bed_bg_sorted.bw
Zfp365_id3573106_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mapkapk3_id3370575_MED13_ES_TAM_bg.bed_bg_sorted.bw
Champ1_id2826164_MED13_ES_TAM_bg.bed_bg_sorted.bw
Tnrc6c_id4011171_MED13_ES_TAM_bg.bed_bg_sorted.bw
Dagla_id5850122_MED13_ES_TAM_bg.bed_bg_sorted.bw
Bahcc1_id4017212_MED13_ES_TAM_bg.bed_bg_sorted.bw
Mex3d_id3604301_MED13_ES_TAM_bg.bed_bg_sorted.bw


title: MED13-13lfl_ES_TAM_rep3_CapC_set1


title: MED13-13lfl_ES_UNT_rep1_CapC_set2