title: mEmBP-OE-4_rep3

city: Shanghai

first: Faming

last: Chen

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Read quality was checked using FastQC.
Adaptor and low quality reads of raw sequencing reads were trimmed using trim_galore. Adaptor of read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; Adaptor of read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Cleaned reads were mapped to the rice reference genome (Os-Nipponbare-Reference-IRGSP-1.0) using STAR 2.5.3a with "--quantMode GeneCounts" option to report the read counts per gene.
Differentially expressed genes were determined using DESeq2 with read counts per gene as input.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene for each sample

source_name: top second leaf of mEmBP-OE-4

growth_protocol: The rice grew at Songjiang breeding stating (30°56′ N, 121°8′ E) of the Shanghai Institutes of Plant Physiology and Ecology, Shanghai, China. Seedlings were transplanted into field and plant spacing was 0.2 m for both row and column.

extract_protocol:
For RNA-sequencing (RNA-seq) analysis, we collected the top second leaves of mEmBP-OE-4 line and WT at early heading stage at about 10:00 a.m. from field grown plants. Four replications of mEmBP-OE-4 line (mEmBP-OE-4_rep1-4) and WT (WT_rep1-4) were collected, respectively. RNA was extracted using the PureLink RNA Mini Kit following manufacturer’s protocol (Life Technologies Corporation).
RNA libraries were prepared for sequencing based on standard Illumina protocols.

tag: sampling time

tag: growing stage

value: Heading stage


title: mEmBP-OE-4_rep4

status: Public on Jan 08 2020

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Oryza sativa

tag: genotype/variation


title: rpn5-ts rep1  [Rpn5_TS_P1_S85]

city: Indianapolis

first: Sarah

last: Peck Justice

state: IN

address: 635 Barnhill Dr

department: Biochemistry and Molecular Biology

country: USA

institute: Indiana University

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC sacCer3
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

organism: Saccharomyces cerevisiae

growth_protocol: YPD; OD ~0.5

extract_protocol:
hot acid phenol; DNAse treated
KAPA mRNA HyperPrep kit

treatment_protocol: no treatment

tag: strain information

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0   lys2Δ0 can1Δ::LEU2-MFA1pr::His3 rpn5-ts::URA3

tag: molecule subtype

value: polyA-enriched RNA


title: mEmBP-OE-4_rep2


title: 10002_cl_1_3_T6

type: RNA

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

hyb_protocol: Equal quantities (325 ng) of Cy3- and Cy5-labeled cRNA targets were mixed and incubated on microarray slides at 65°C for 17 hours.

scan_protocol: After washing, slides were scanned using the Microarray Scanner (G2565CA, Agilent Technologies) at 5-µm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

data_processing:
The data were extracted from these images using the Agilent Feature Extraction 10.7.3.1. software.
Data were computed using the Genespring GX version 12.6 ( Agilent Technologies), a web-based tool suite that allows integrated analysis of two-color microarrays. Arrays were background corrected using minimum method (any intensity which is zero or negative after background subtraction is set equal to half the minimum of the positive corrected intensities for that array), and a within-array loess normalization were performed. Finally, array data were normalized using quantile normalization. Log intensity ratios for each spot were obtained with background subtraction.

organism: Aspergillus nidulans

source_name: Total Mycelium

label_protocol: Target preparation and hybridization were done according to the manufacturer’s instructions. Briefly, 200 ng of total RNA was labeled using the Low Input Quick Amp Labeling Kit, 2 colors (Agilent Technologies), Cy5-CTP for the reference RNA made of a mix of all samples, and Cy3-CTP for individual samples. Internal standards were derived from the Two-Color RNA Spike-in Kit (Agilent Technologies). The labeled targets were purified using the RNeasy® Mini Kit (Qiagen) and their quality and quantity were confirmed by spectrophotometry and the Bioanalyzer 2100 technology (Agilent Technologies).

growth_protocol: Two independent series of quadruplicate cultures from A. nidulans CV125 strain were grown in liquid culture medium with 0,007% Roundup for 15 h at 30°C with agitation at 150 rpm. Total Mycelium was harvested from each culture,  immediately frozen in  liquid nitrogen and stored at -80°C.

extract_protocol: Extraction of total RNA started by protein denaturation in guanidine 6 M, sodium acetate 20 mM pH 5 and dithiotreitol 1 mM. After a 15-min centrifugation at 10000 rpm, +4°C, supernatant was filtered to remove cell debris, and  RNA was precipited by 2-hours incubation in 2,5 volumes of ethanol 95% at -20°C. These steps were repeated and RNA extract was stored in 1.5 ml of ethanol 70% with sodium acetate 100 mM at -80°C until use. Further purification was performed from 25% volume of each alcoholic RNA extract, by high-speed centrifugation followed by three washes of the pellet with 75% ethanol before solubilization in 250 µL RNase-free water, then extraction of impurities with 900 µL TRIzol® (Life Technologies) according to the manufacturer's instructions. After precipitation in 500 µL isopropanol at room temperature, RNA was pelleted by high-speed centrifugation and the pellet washed twice with 75% ethanol, then solubilized in 100 µL RNase-free water and stored at -80°C until molecular analyses.

tag: strain

tag: biological replicate

tag: treatment

value: Control

tag: array slide

tag: reference

value: Reference RNA (mixed samples)


title: 10002_cl_1_2_R2

treatment_protocol: A. nidulans CV125 strain were grown in liquid culture medium with 0,007% Roundup for 15 h at 30°C with agitation at 150 rpm

value: Roundup


title: 10002_cl_1_1_T4


title: RnRC2

city: Malaga

first: Maria

middle: Clara

last: Pliego

state: Malaga

address: Cortijo de la Cruz s/n

country: Spain

institute: IFAPA Centro de Malaga

data_processing:
Basecalls performed using Illumina CASAVA
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Genomics Workbench ver.10.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Genomics Workbench ver.10.0
Genome_build: Rnecatrix_2.0
Supplementary_files_format_and_content: Normalized expression values

organism: Rosellinia necatrix

source_name: mycelium

growth_protocol: In RnPDA samples Rosellinia necatrix were grown 5 days at 25ºC on potato dextrose agar (PDA; Difco Laboratories, Detroit). In RnRC samples Rosellinia necatrix mycelium were grown 5 days at room temperature on avocado roots.

extract_protocol:
Mycelium was collected and frozen in liquid nitrogen and was macerated in a mortar with a small amount of sand and liquid nitrogen. After macerating, the powder was collected in a 2 ml eppendorf up to half and resuspended in 1 ml of denaturation solution for the isolation of RNA (Fluka; Switzerland) and saturated phenol pH 4.3 (1:1) plus 7 µl of β-Mercaptoethanol. 100 µl of chloroform was added and mixed well by vortexing, samples were incubated 3 min at room temperature, and centrifuged at 12000 g for 10 min at 4 ºC. The aqueous phase was collected for downstream steps. Total RNA was extracted  using NucleoSpin RNA plant kit (Macherey-Nagel, Germany), following the instructions provided by the manufacturer.
Libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina Inc) according to the protocols recommended by the manufacturer.

tag: genotype

value: wild type

value: grown on avocado roots

tag: tissue

value: mycelium


title: scRNA-seq of HUVEC in FM [103350-001-001_S1]

city: Frankfurt

first: David

last: John

state: Hessen

address: Theodor-Stern-Kai 7

country: Germany

institute: Institute for Cardiovascular Regeneration

description:
ScRNA-SEQ of HUVEC in full medium
processed data file: inVitro_FM-vs_EndMT_Expressionmatrix.csv

data_processing:
Chip-Seq: The samples were sequenced on  Illumina NextSeq hardware and assessed for quality using FastQC (Andrews S. 2010,  FastQC: a quality control tool for high throughput sequence data. Available online at:  http://www.bioinformatics.babraham.ac.uk/projects/fastqc) or used for qRT-PCR analysis  with the primers described before. Reads were trimmed using fastx-trimmer  (http://hannonlab.cshl.edu/fastx_toolkit/). Trimmed sequences were mapped to the  GRCH38 version of the human genome with STAR 2.4.2a 4 using only unique alignments  to exclude reads with unclear placing. PCR duplicates were removed using Picard 1.136  (Picard: A set of tools (in Java) for working with next generation sequencing data in the  BAM format; http://broadinstitute.github.io/picard/) to avoid PCR artefacts leading to  multiple copies of the same original fragment. Peaks were called using homer findPeaks  version 4.0311 with parameter –region to combine close peaks. The minimum distance and size of peaks for H3K9me3 were set to -size 2000 and –minDist 10000
Data were filtered using the following specifications:
RNA:SEQ: Base calling and FASTQ were done with  Illumina's HiSeq Control Software version 1.5.15.1 (RTA v1.13.18 and bclfastq v1.8.3).  Sequenced reads were mapped to the mouse reference genome with TopHat version  2.0.5, and differentially expressed genes were assessed by use of Cuffdiff, a part of the  Cufflinks version 2.1.1 package.
Cellular suspensions were loaded on a 10X Chromium Controller (10X Genomics) according to manufacturer’s protocol based on the 10X Genomics proprietary technology13. HUVEC study and murine scRNA-seq libraries were prepared using Chromium Single Cell 3′ v2 Reagent Kit and Chromium Single Cell 3′ v3 Reagent Kit, respectively (10X Genomics), according to manufacturer’s protocols. Briefly, the initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10X cell barcodes, UMI (unique molecular identifiers) and poly(dT) sequences. Reverse transcription reactions were engaged to generate barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). Bulk cDNA was amplified using a Biometra Thermocycler Professional Basic Gradient with 96-Well Sample Block (98°C for 3 minutes; cycled 14×: 98°C for 15 s, 67°C for 20 s, and 72°C for 1 minute; 72°C for 1 minute; held at 4°C). Amplified cDNA product was cleaned with the SPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3′ v2 and Chromium Single Cell 3′ v3 Reagent Kits as follows: fragmentation, end repair and A-tailing; size selection with SPRIselect; adaptor ligation; post-ligation cleanup with SPRIselect; sample index PCR and cleanup with SPRI select beads. Library quantification and quality assessment was performed using Bioanalyzer Agilent 2100 using a High Sensitivity DNA chip (Agilent Genomics). Indexed libraries were equimolarly pooled and sequenced using paired-end 26x98bp as sequencing mode by GenomeScan (Leiden, Netherlands). Single-cell RNA-seq outputs were processed using the Cell Ranger (10X Genomics) suite versions 2.1.1 (in vitro HUVEC samples) or 3.0.1 (in vivo 3d AMI samples). HUVEC in vitro data has been mapped to the GRCh38 (version 1.2.0) reference genome by using the “count” function. Subsequently, individual processed datasets have been merged with “aggregate”. Secondary analysis was conducted using the Seurat 2.3.4 package in R.14 We filtered the data for cells expressing at least 200 genes. Moreover, we aimed to avoid doublets by removing cells with high unique molecular identifier (UMI) counts (> 90000) and high number of genes (> 8000). We also accounted for possible dead cells and removed cells with high mitochondrial content (> 10 % of total UMI). The remaining matrix was log-normalized and scaled. After detecting variable genes, a principal component analysis (PCA) using 10 dimensions was applied. Clustering of the cells was then performed by Seurat’s FindCluster function with 0.6 resolution. We used t-distributed stochastic neighbor embedding (t-SNE) to visualize cell clusters.15 We applied a generic threshold of 2.5 to the scaled value of all candidate genes to separate high and low or no expressing cells. Accordingly, in vivo 3d AMI data we mapped against the mm10 (version 3.0.0) reference genome using Cell Ranger “count”. In Seurat 2.3.4 we applied similar filters for removing cells with high and low UMI counts but removed the upper 5 % and lower 1 % of all cells per individual sample. High mitochondrial content cells (>10 %) were removed similarly. We only kept genes that showed at least in 2 cells an UMI count of more than 1. We merged the data and counted cells expressing at least 1 UMI for Cdh5 and Pecam1 (ECs) as well as Cdh5, Pecam1 and two mesenchymal markers (EndMT cells) between the libraries.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene_expression.tsv was generatedby cuffdiff and assembled by cummerbund; ChIP-seq bed files

molecule: polyA RNA

organism: Homo sapiens

source_name: ScRNA-SEQ of HUVEC in full medium

growth_protocol: Experiments were performed using human umbilical vein endothelial cells (HUVEC) purchased from Lonza. Cells were cultured in endothelial basal medium without phenol red (#C-22215, PromoCell), supplemented with hydrocortisone (#CC-4035C, Lonza), ascorbic acid (#CC-4116C, Lonza), bovine brain extract (BBE) (#CC-4092C, Lonza), epidermal growth factor (EGF) (#CC-4017, Lonza), 10% fetal bovine serum (FBS) (#CC-4101, Lonza) and GA-1000 (Gentamicin+Amphotericin-B, CC-4081C, Lonza) or for EndMT without EGF and BBE.

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (#79306; Qiagen) and miRNeasy-kit (#217004; Qiagen) with additional DNase I (#79254; Qiagen) digestion according to the manufacturer’s protocol. 1 μg of RNA from each sample was reverse-transcribed using random hexamer primed single-strand cDNA (10 min at 25 °C, 15 min at 42 °C, 5 min at 99 °C) by MMLV Reverse Transcriptase (#N8080018; Life technologies) as previously described. (Boeckel et al., 2011). For qPCR, cDNA was amplified using Fast SYBR Green Mastermix (#4385612 Life Technologies) on a ViiA7- Realtime qPCR System (Life Technologies). Expression level of mRNAs were normalized to RPLP0 which served as a housekeeping gene using the 2‑ΔCt method.
900ng of total RNA was used as input for whole transcriptome RNA-seq library preparation (TruSeq® Stranded Total RNA, Illumina) following low throughput protocol. Sequencing was performed on Illumina Nextseq 500 (Illumina) using V2 chemistry and 75bp single-end setup.

treatment_protocol: 4 x 10^5 HUVEC were seeded in a 60 mm cell culture dish, cells were cultivated either full medium (FM) or in differentiation media (DM).  After 24 h of cultivation, cells were treated with 10 ng/ml TGF-β2 (#302-B2, R&D System). After additional 48 h of incubation, the treatment was repeated. 96h later, RNA was isolated.

value: Wild-type

tag: cell type

tag: passages

value: full medium (FM)


title: il7 mutant rep 3

city: Freiburg im Breisgau

first: Thomas

last: Boehm

address: Stübeweg 51

department: Immunology

institute: MPI-IE Freiburg

description:
processed data files:
DESeq2.counts_normalized.tsv
kidney.DESeq2.results.tsv
il7_17A_kidney_mut3

data_processing:
Basecalling was performed with Illumina HiSeq Control Software/RTA2. Libraries were demultiplexed with bcl2fastq version: 2.17.1.14 .
Reads were aligned to the GRCz10 genome assembly using STAR-2.5.3a with the following settings: annotated splice junctions were based on modified Ensembl release 88 GTF file, maximum intron size was set to 11000 and RAM limit for BAM file sorting to 45216384578. The GTF file was modified such that a gene model for putative zebrafish il2 based on XM_009300745.2 has been appended to the original ensembl v.88 GTF.
The number of reads per annotated gene (based on Ensembl 88 zebrafish gene annotation extended with putative zebrafish il2 gene model) were counted with featureCounts version 1.5.2. Fragments were only counted if both ends aligned on the same chromosome (-C and -B options) with a minimum mapping quality of 10 and in agreement with the strand orientation of the annotated gene (library type 2). Only primary alignments were counted.
Differential gene expression analysis was performed with Bioconductor package DESeq2 version 1.14.1. Differentially expressed genes were filtered at absolute logFC >=1 and FDR < 5%.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text files include differential gene expression results generated by DESeq2. Tab-delimited text files include deph-normalized counts output by DESeq2.

organism: Danio rerio

source_name: whole kidney marrow cells

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma) following the  manufacturer's instructions. After treatment with Cloned DNaseI (Takara),  RNA extraction using TRI Reagent was repeated. RNA quality was determined using the 2100 Bioanalyzer instrument (Agilent) and RNA concentration was determined using Qbit 2.0 Fluorometer (Life Technologies).
RNA libraries were prepared for sequencing using the TruSeq stranded total RNA sample preparation with Ribo-Zero Human/Mouse/Rat (RS-122-2203).

value: whole kidney marrow

value: il7:internal deletion of exons 2-4

tag: background strain

value: TLEK

tag: surface phenotype

value: unfractionated cells


title: pup2-ts rep3 [Pup2_TS_RNA_P3_DNAse_S83]

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0   lys2Δ0 can1Δ::LEU2-MFA1pr::His3 pup2-ts::URA3


title: RnRC1


title: WT_rep3

source_name: top second leaf of WT


title: mEmBP-OE-4_rep1


title: pup2-ts rep1 [Pup2_TS_P1_S81]


title: pup2-ts rep2 [Pup2_TS_P2_S82]


title: il7 mutant rep2

description:
processed data files:
DESeq2.counts_normalized.tsv
kidney.DESeq2.results.tsv
il7_17A_kidney_mut2


title: WT_rep4


title: WT rep4 [WT_By4741_RNA_P4_DNAse_S80]

source_name: WT

value: WT

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: il7 mutant rep1

description:
processed data files:
DESeq2.counts_normalized.tsv
kidney.DESeq2.results.tsv
il7_17A_kidney_mut1


title: control rep 3

description:
processed data files:
DESeq2.counts_normalized.tsv
kidney.DESeq2.results.tsv
il7_17A_kidney_wt3

value: wt


title: WT rep3 [WT_By4741_RNA_P3_DNAse_S79]

value: polyA-enriched RNA


title: WT rep2 [WT_p2_S78]


title: pup2-ts rep4 [Pup2_TS_RNA_P4_DNAse_S84]


title: WT_rep1

value: Heading stage


title: PBMC, Cold, replicate 2

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy5 samples were pooled on a equimolar basis and served as reference pool, and individual Cy3-labelled samples were hybridized against the reference pool.

hyb_protocol: Hybridization was performed by preparing a cRNA target solution containing 1.875 ng Cy3-labeled cRNA, 1.875 ng Cy5-labeled pool cRNA, 25 μl of 10Xblocking agent, 5 μl 25X Fragmentation Buffer in a total volume of 125 μl. The samples were incubated at 60 ºC for 30 min, and then immediately cooled on ice for one minute. After that, 125 μl 2x GEx hybridization buffer HI-RPM was added and hybridized on 2x400k G4861A whole genome Agilent arrays (Agilent Technologies, Inc., Santa Clara, CA, USA) for 17h at 65 ºC in Agilent hybridization chambers in an Agilent hybridization oven rotating at 10 rpm. After hybridization, the arrays were subsequently washed with GE wash buffer 1, for 1 min at room temperature, and GE wash buffer 2, for 1 min at approximately 37 ºC, according to manufacturers protocol (Agilent Technologies).

scan_protocol: The arrays were scanned with an Agilent Microarray Scanner (Agilent Technologies Scanner G2505C US22502548, Agilent Tecnologies) with a Profile AgilentG3_GX_2Color.

data_processing: Data were exported into GeneMaths XT 2.12 (Applied Mathematics, Sint-Martens-Latem, Belgium) for background correction and normalization.

organism: Mustela putorius furo

source_name: PBMC

label_protocol: 0.2 mg RNA of each sample was reverse transcribed using the Agilent Low Input Quick Amp Labeling kit (Agilent), according to the manufacturer’s protocol with some modifications (all materials and reagents are from Agilent Technologies, Palo Alto, CA, US). Half of the cDNA sample (5μl) was used for linear RNA amplification and labeling with Cy5 or Cy3. All reactions were performed using half of the amounts indicated by the manufacturer (van Schothorst et al., 2007). Briefly, a transcription master mix was prepared (0.375 μl nuclease-free water; 1.6 μl 5 X Transcription buffer;  0.3 μl 0.1 M DTT; 0.5 μl NTP mix; 0.115 μl T7 RNA Polymerase Blend and 0.12 cyanine 3-CTP or cyanine 5-CTP per sample) was added to 5 μl cDNA.  In vitro transcription and labeling were carried out at 40 ºC for 2 h. The labeled cRNA samples were purified using Qiagen Rneasy minispin columns (Qiagen, Venlo, The Netherlands). Dye incorporation and cRNA concentration was measured using the microarray measurement of the Nanodrop spectrophotometer (NanoDrop Technologies). Yield of each individual sample was 1.875ng and specific activity 6.0 pmol Cy3 or Cy5 per μg cRNA. Two PBMC Cy5 samples showed not enough yield, which were therefore excluded from inclusion in the reference pool. All approved high quality Cy5 cRNA’s were pooled to serve as standard reference pool; the pool consisted of RNA isolated from different tissues to increase signal distribution over all probes.

extract_protocol: Total RNA from PBMC samples was extracted using Tripure Reagent (Roche Diagnostics, Barcelona, Spain). RNA samples were purified with E.Z.N.A. MicroElute RNA Clean Up (Omega Biotek, Vermont, USA), and with 3M sodium acetate and absolute ethanol. RNA yield was quantified using a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the integrity was measured on an Agilent 2100 Bioanalyzer with RNA 6000 Nano chips (Agilent Technologies, South Queensferry, United Kingdom).

treatment_protocol: Male Ferrets (Mustela Putorius Furo from Cunipic, Lleida, Spain) of 3 months of age were used. Ferrets were distributed into two groups (n=7): a control group, acclimatized to room temperature (22±2ºC), and a cold group, acclimatized to 4ºC for 1 week. The animals were weighed before and after cold exposure. Cold-exposed animals were housed individually. All animals were exposed to a light/dark cycle os 12 h and had free acces to water and diet (Gonzalo Zaragoza Manresa SL, Alicante, Spain). The animals were anesthetized using 10mg/kg of Ketamine hydrochloride (Imalgène 1000, Merial Laboratorios SA, Lyon, France) and 80 mg/kg medetomidine (Domtor, Orion Pharma, Espoo, Finland), and sacrificed by exsanguination after cardiac punction. Different white adipose tissue depots (inguinal and periaortic), were rapidly removed and weighed, frozen in liquid nitrogen and stored at -80ºC until RNA analysis.                                                                                Troncular blood was collected from heart. Blood samples (500 μl) were stored 1h at 4ºC and were then centrifuged at 1000 g for 10 min to collect the serum. Additional blood samples (5-6 ml) were collected in ad libitum conditions from heart, using heparin in NaCl (0.9%) as anticoagulant and used for PBMC isolation by Ficoll gradient separation, according to the instructions indicated by manufacturer (GE Healthcare Bio Sciences, Barcelona, Spain), with some modifications. Briefly, the anticoagulant-treated blood was diluted with an equal volume of balanced salt solution, which was prepared by mixing two stock solutions (1/10); solution A (5.5 mM anhydrous D-glucose, 5 mM CaCl2 2H2O, 0.98 mM MgCl2 6H2O, 5.4 mM KCl, 145 mM Tris) and solution B (140 mM NaCl). Afterwards, the blood was layered carefully over Ficoll without intermixing (1.5 ml of Ficoll for 2 ml of blood mixed with balanced salt solution) in a centrifuge tub and centrifuged at 900g for 40 min at 20ºC. PBMC, together with platelets, were harvested from the interface between Ficoll and sample layers. This material was then centrifuged in balanced salt solution at 400 g for 10 min at 20ºC to wash PBMC and to remove the platelets.

value: PBMC

tag: gender

value: male

tag: age

value: 3 months

source_name: PBMC mixed with other tissues

value: PBMC mixed with other tissues


title: WT rep1 [WT_p1_S77]


title: PBMC, Cold, replicate 4


title: conrol rep 2

description:
processed data files:
DESeq2.counts_normalized.tsv
kidney.DESeq2.results.tsv
il7_17A_kidney_wt2


title: control rep 1

description:
processed data files:
DESeq2.counts_normalized.tsv
kidney.DESeq2.results.tsv
il7_17A_kidney_wt1


title: PBMC, Cold, replicate 3


title: WT_rep2

value: wild type

tag: sampling time

tag: growing stage


title: siCyclink#2-3

status: Public on Jan 07 2020

city: Hubei,China

first: Yao

last: Guojun

address: Hubei,China

institute: Hua Zhong University of science and technology

data_processing:
sequencing libraries were validated using Agilent DNA 100 kit with Agilent Bio analyzer 2100.
The libraries were normalized, and pooled for sequencing, with Illumina HiSeq Xten system using the paired end 150 bp
Illumina data analysis pipeline was then used for sequence analysis. All samples were allocated to lanes and processed in blinded fashion to keep bias to a minimum
Supplementary_files_format_and_content: Calculate the expression read count using the Stringtie-1.3.3b software. Then, the gene and transcript FPKM were calculated.

growth_protocol: Cells were cultivated in PRMI-1640 medium with 10% FBS and 100 μg/mL penicillin and streptomycin in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Invitrogen), and concentration was determined using Nanodrop spectrophotometer (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were transfected with control or Cyclin K-targeting siRNAs for 48 h. Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

value: Lung cancer cell line

tag: cell line

value: siCyclinK


title: siCyclinK#2-2


title: siCyclinK#2-1


title: siCyclinK#1-3


title: PBMC, Cold, replicate 1


title: PBMC, Control, replicate 4


title: PBMC, Control, replicate 5


title: PBMC, Control, replicate 6


title: siCtrl-1

value: siCtrl


title: PBMC, Control, replicate 3


title: siCyclinK#1-2


title: PBMC, Control, replicate 2


title: siCtrl-2


title: siCtrl-3


title: MG24H_Input_all_reps

city: RTP

first: Trevor

last: Archer

address: 111 TW Alexander

institute: NIH

description: ChIP-Seq

library_source: genomic

data_processing:
Aligned with bowtie version 1.2 and parameters: -v 1 -m 1 --best --strata
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: coverage per 10 million mapped reads

molecule: genomic DNA

growth_protocol: MCF-7 cells were grown in a humidified incubator at 37°C with 5% CO2 in MEM, supplemented with 10% fetal bovine serum 100 μg/mL penicillin/streptomycin, 2 mM glutamine and 10 mM HEPES. For MG132 treatment, cells were seeded overnight in phenol red-free MEM supplemented with 5% charcoal-stripped calf serum and 2 mM glutamate. Next day, cells were treated with, vehicle (DMSO) or 1uM MG132 for 4 or 24 hours.

extract_protocol:
ChIP DNA was collected from MCF7 cells cultured in phenol red free MEM, supplemented with charcoal stripped serum and containing  0.1% DMSO or 1 uM MG132 for 4 or 24H.  Cells were incubated for 4 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.
NEXTFlex Rapid DNA-Seq Kit   BIOO Scientific  Cat#5144-02

value: breast cancer cells

tag: chip antibody

value: none (input)


title: MG24H_PolIISer5_rep2

description: ChIP-Seq

tag: chip antibody info.

value: Abcam Ab5131


title: MG24H_PolII8WG16_rep1

description: ChIP-Seq

value: Santa Cruz Biotechnology Sc-56767


title: MG24H_PolIISer5_rep1

description: ChIP-Seq


title: MG24H_PolIISer2_rep2

description: ChIP-Seq

value: Abcam Ab5095


title: MG24H_PolIISer2_rep1

description: ChIP-Seq


title: PBMC, Control, replicate 1


title: MG4H_Input_all_reps

description: ChIP-Seq


title: MG4H_PolII8WG16_rep2

description: ChIP-Seq


title: MG4H_PolIISer5_rep2

description: ChIP-Seq


title: MG4H_PolIISer5_rep1

description: ChIP-Seq


title: MG4H_PolIISer2_rep1

description: ChIP-Seq


title: MG4H_PolIISer2_rep2

description: ChIP-Seq


title: UNTR_PolII8WG16_rep1

description: ChIP-Seq

value: Vehicle


title: UNTR_PolII8WG16_rep2

description: ChIP-Seq


title: PIGS-KO cells

city: Osaka

first: Taroh

last: Kinoshita

address: ３-3-1 Yamadaoka, Suita, Osaka

country: Japan

institute: Research Institute for Microbial Diseases

description: Gene expression data from HEK293-PIGS-KO cells

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hr at 45˚C on Clariom S Array, Human. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: biotin

source_name: HEK293-PIGS-KO cells (Control)

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit Thermo Fisher Scientific) following the manufacturer's instructions.

growth_protocol: HEK293-PIGS-KO and HEK293-PIGS-UBE2J1-DKO cells were grown in Dulbecco's Modified Eagle Medium with 10% Fetal Bovine Serum overnight and harvested for total RNA extraction.

extract_protocol: Total RNA were extracted with RNeasy Mini Kit (Qiagen) according to the manufacture’s instructions.

treatment_protocol: Knockout of genes using CRISPR/Cas9


title: MG24H_Input_allreps

extract_protocol:
MNase digested ChIP DNA was collected from MCF7 cells cultured in phenol red free MEM, supplemented with charcoal stripped serum and containing  0.1% DMSO or 1 uM MG132 for 4 or 24H.  Cells were incubated for 4 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.
NEXTFlex Rapid DNA-Seq Kit   BIOO Scientific  Cat#5144-02

value: allreps


title: UNTR_PolIISer5_rep1

description: ChIP-Seq


title: UNTR_PolIISer2_rep1

description: ChIP-Seq


title: MG24H_H3K914ac_rep2

value: Cell Signaling Technology CST#9677


title: MG24H_TotalH3_allreps

value: Abcam  Ab1791


title: MG24H_H3K914ac_rep1


title: PBMC_healthy_scATAC

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Fastqs were demultiplexed using CellRanger-ATAC mkfastq (v1.0.0)
Sequencing reads were aligned the hg19 reference using CellRanger-ATAC count (v1.0.0). Single-cells were called using the default parameters from this step.
Barcode multiplets were determined using bap2 (v0.7.0)
Genome_build: hg19
Supplementary_files_format_and_content: Processed fragment files from 10x CellRanger-ATAC count

source_name: Peripherial blood mononuclear cells

extract_protocol: 10x Genomics scATAC-seq

value: Peripherial blood mononuclear cells

tag: enrichment


title: MG24H_H3K122ac_rep3

tag: treatment

value: Abcam Ab33309


title: siCyclinK#1-1


title: MG24H_H3K122ac_rep1


title: MG24H_H3K27ac_rep2

value: Abcam Ab4729


title: MG24H_H3K122ac_rep2


title: PIGS-UBE2J1-DKO cells

description: Gene expression data from HEK293-PIGS-UBE2J1-DKO cells

source_name: HEK293-PIGS-UBE2J1-DKO cells (Sample)


title: MG24H_H3K36me3_rep1

value: Abcam  Ab9050


title: MG24H_H3K36me3_rep3


title: MG24H_H3K36me3_rep2


title: MG24H_H3K27ac_rep1


title: MG24H_H3K4me3_rep1

value: Active Motif Cat#39159


title: MG4H_Input_allreps


title: MG4H_TotalH3_allreps


title: MG4H_H3K914ac_rep1


title: MG4H_H3K122ac_rep3


title: MG4H_H3K122ac_rep2


title: MG4H_H3K122ac_rep1


title: MG4H_H3K27ac_rep1


title: MG4H_H3K27ac_rep2


title: MG4H_H3K36me3_rep3


title: MG4H_H3K36me3_rep2


title: MG4H_H3K4me3_rep1


title: MG24H_H3K4me3_rep2


title: MG4H_H3K36me3_rep1


title: MG4H_H3K4me3_rep2


title: UNTR_Input_allreps


title: T1D+T1D-NET_KUB/I02604_Quantile

city: Prague

first: Adam

last: Klocperk

address: V Uvalu 84

department: Department of Immunology

country: Czech Republic

institute: University Hospital in Motol

description: T1D moDC+ T1D-NET 4

data_processing:
Approximately 21 million reads before and 17 million reads per sample after mapping. RNAseq reads were trimmed for adapters using cutadapt (version 1.8.1) while low quality signals were removed using the fastq illumina filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter).
Reads shorter than 50bp were omitted from further analysis. Subsequent mapping to the human reference genome GRCh38 was performed using TopHat (version 2.0.14).
Gene expression counts were quantified using HTSeq.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx file with samples represented by columns, transcripts as rows.

source_name: moDC derived from monocytes of T1D patient 4 cultivated with autologous T1D NETs

growth_protocol: moDCs were generated from PBMC after 2h adherence. Adhered monocytes were cultivated in presence IL-4 and GM-CSF in serum free culture medium for 6 days.

extract_protocol:
106 moDC/ml from HD (healthy donors) were cultivated with1,000ng/ml of autologous HD-NETs, with T1D-NETs or left untreated for 8 hours. Similarly, 106 moDCs/ml from T1D were also cultivated with1,000ng/ml of autologous T1D-NETs, HD-NETs or left untreated for 8 hours. The cells were then washed and lysed using RLT buffer (Qiagen, Hilden, Germany). Total RNA was isolated using RNeasy Mini Kit following manufacturer’s instructions (Qiagen), RNA quality and quantification was determined by TapeStation 4200 (Agilent, St. Clara, USA) following manufacturer’s instructions.
Library construction was conducted employing the Illumina True Seq stranded mRNA Poly A protocol and subsequently sequenced using a HiSeq 4,000 (1x50bp single end reads, 15 samples per lane)

treatment_protocol: 1M/ml moDC were cultivated with 1000ng/ml DNA contained in NETs

tag: disease state

value: type 1 diabetes

value: monocyte-derived dendritic cells


title: T1D+HDo-NET_LUK/I02620_Quantile

description: T1D moDC+ HD-NET 5

source_name: moDC derived from monocytes of T1D patient 5 cultivated with healthy NETs


title: T1D+T1D-NET_HER/I02616_Quantile

description: T1D moDC+ T1D-NET 2

source_name: moDC derived from monocytes of T1D patient 2 cultivated with autologous T1D NETs


title: T1D+HDo-NET_KUB/I02605_Quantile

description: T1D moDC+ HD-NET 4

source_name: moDC derived from monocytes of T1D patient 4 cultivated with healthy NETs


title: T1D+T1D-NET_FUR/I02601_Quantile

description: T1D moDC+ T1D-NET 1

source_name: moDC derived from monocytes of T1D patient 1 cultivated with autologous T1D NETs


title: T1D+HDo-NET_HER/I02617_Quantile

description: T1D moDC+ HD-NET 2

source_name: moDC derived from monocytes of T1D patient 2 cultivated with healthy NETs


title: T1D+T1D-NET_KOS/I02613_Quantile

description: T1D moDC+ T1D-NET 3

source_name: moDC derived from monocytes of T1D patient 3 cultivated with autologous T1D NETs


title: MG4H_H3K914ac_rep2


title: T1D+T1D-NET_LUK/I02619_Quantile

description: T1D moDC+ T1D-NET 5

source_name: moDC derived from monocytes of T1D patient 5 cultivated with autologous T1D NETs


title: UNTR_H3K914ac_rep2


title: UNTR_H3K914ac_rep1


title: T1D+HDo-NET_KOS/I02614_Quantile

description: T1D moDC+ HD-NET 3

source_name: moDC derived from monocytes of T1D patient 3 cultivated with healthy NETs


title: UNTR_TotalH3_allreps


title: UNTR_H3K122ac_rep3


title: UNTR_H3K122ac_rep1


title: UNTR_H3K122ac_rep2


title: T1D_Unstim_LUK/I02618_Quantile

description: T1D moDC 5

source_name: moDC derived from monocytes of T1D patient 5


title: T1D_Unstim_KUB/I02603_Quantile

description: T1D moDC 4

source_name: moDC derived from monocytes of T1D patient 4


title: T1D+HDo-NET_FUR/I02602_Quantile

description: T1D moDC+ HD-NET 1

source_name: moDC derived from monocytes of T1D patient 1 cultivated with healthy NETs


title: T1D_Unstim_KOS/I02612_Quantile

description: T1D moDC 3

source_name: moDC derived from monocytes of T1D patient 3


title: UNTR_H3K27ac_rep2


title: MG24H_PolII8WG16_rep2

description: ChIP-Seq


title: T1D_Unstim_HER/I02615_Quantile

description: T1D moDC 2

source_name: moDC derived from monocytes of T1D patient 2


title: HDo+T1D-NET_Z30/I02608_Quantile

description: HD moDC+ T1D-NET 5

source_name: moDC derived from monocytes of healthy donor 5 cultivated with T1D NETs

value: healthy


title: UNTR_H3K27ac_rep1

value: breast cancer cells


title: UNTR_H3K36me3_rep3


title: T1D_Unstim_FUR/I02600_Quantile

description: T1D moDC 1

source_name: moDC derived from monocytes of T1D patient 1


title: UNTR_H3K36me3_rep2


title: UNTR_H3K36me3_rep1


title: UNTR_H3K4me3_rep2


title: HDo+T1D-NET_M40/I02599_Quantile

description: HD moDC+ T1D-NET 3

source_name: moDC derived from monocytes of healthy donor 3 cultivated with T1D NETs


title: HDo+T1D-NET_Z10/I02593_Quantile

description: HD moDC+ T1D-NET 4

source_name: moDC derived from monocytes of healthy donor 4 cultivated with T1D NETs


title: HDo+T1D-NET_M30/I02596_Quantile

description: HD moDC+ T1D-NET 2

source_name: moDC derived from monocytes of healthy donor 2 cultivated with T1D NETs


title: UNTR_H3K4me3_rep1


title: HDo+HDo-NET_Z30/I02607_Quantile

description: HD moDC+ HD-NET 5

source_name: moDC derived from monocytes of healthy donor 5 cultivated with autologous healthy NETs


title: HDo+HDo-NET_Z10/I02592_Quantile

description: HD moDC+ HD-NET 4

source_name: moDC derived from monocytes of healthy donor 4 cultivated with autologous healthy NETs


title: ATAC-seq_Bcat_Cultured_R1

city: Baltimore

first: Mark

middle: F

last: Sabbagh

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
ATAC-seq data were aligned to the GRCm38 genome using HISAT2 version 2.1.0 (hisat2 -t -X 2000 --no-mixed --no-discordant) and then duplicate reads were removed (picard MarkDuplicates). Peaks were called using MACS2 version 2.1.2 (callpeak -f BAM --nomodel --keep-dup all --shift −100 --extsize 200) (Zhang et al., 2008). Peaks were then filtered for fold-change >2 and -log(qvalue) >2. deepTools was used to visualize ATAC-seq peaks on the browser (bamCoverage -bs 1 –extendReads --ignoreDuplicates --normalizeUsing CPM).
Genome_build: mm10

organism: Mus musculus

source_name: 8-day primary cultures of beta-catenin stabilized puromycin-purified brain ECs

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
For ATAC-seq, ~50,000 GFP-positive FACS-sorted cells or trypsinized cultured ECs were gently centrifuged and then resuspended in ice-cold lysis buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 0.1% Igepal CA-630) and immediately centrifuged at 500 x g for 10 min at 4°C to prepare nuclei. The resulting nuclear pellet was resuspended in a 50 ul reaction volume in Tn5 transposase and transposase reaction buffer (FC-121–1030, Illumina Inc, San Diego, CA), and the tagmentation reaction was incubated at 37°C for 30 min.
Tagmented DNA was purified using QIAGEN MinElute Gel Extraction kit (28604, Qiagen). ATAC-seq libraries were PCR amplified for 11 cycles. Agencourt AMPure XP beads (A63880, Beckman Coulter) were used to purify ATAC-seq libraries, which were then paired-end sequenced for 36 cycles on a NextSeq500 (Illumina).

tag: strain/genotype

value: Adult

tag: Sex

value: Male

value: Brain

tag: cell-type

value: Vascular endothelial cells


title: ATAC-seq_WT_Cultured_R6

source_name: 8-day primary cultures of puromycin-purified brain ECs

tag: tissue


title: ATAC-seq_Bcat_Cultured_R2


title: ATAC-seq_WT_Cultured_R5


title: HDo+HDo-NET_M40/I02598_Quantile

description: HD moDC+ HD-NET 3

source_name: moDC derived from monocytes of healthy donor 3 cultivated with autologous healthy NETs

tag: cell type


title: ATAC-seq_WT_Cultured_R4


title: HDo+HDo-NET_M30/I02595_Quantile

description: HD moDC+ HD-NET 2

source_name: moDC derived from monocytes of healthy donor 2 cultivated with autologous healthy NETs


title: HDo+HDo-NET_M20/I02610_Quantile

description: HD moDC+ HD-NET 1

source_name: moDC derived from monocytes of healthy donor 1 cultivated with autologous healthy NETs


title: HDo_Unstim_Z30/I02606_Quantile

description: HD moDC 5

source_name: moDC derived from monocytes of healthy donor 5


title: HDo_Unstim_Z10/I02591_Quantile

description: HD moDC 4

source_name: moDC derived from monocytes of healthy donor 4


title: ATAC-seq_WT_Cultured_R3


title: ATAC-seq_WT_Cultured_R2


title: HDo_Unstim_M40/I02597_Quantile

description: HD moDC 3

source_name: moDC derived from monocytes of healthy donor 3


title: ATAC-seq_Adult_Brain_GFPpos_R2

source_name: Adult GFP-positive sorted cells from brain


title: HDo_Unstim_M30/I02594_Quantile

description: HD moDC 2

source_name: moDC derived from monocytes of healthy donor 2


title: ATAC-seq_WT_Cultured_R1


title: ATAC-seq_Adult_Cerebrum_GFPpos_R2

source_name: Adult GFP-positive sorted cells from cerebrum

value: Cerebrum


title: HDo_Unstim_M20/I02609_Quantile

description: HD moDC 1

source_name: moDC derived from monocytes of healthy donor 1


title: ATAC-seq_Adult_Cerebrum_GFPpos_R1


title: HDo+T1D-NET_M20/I02611_Quantile

description: HD moDC+ T1D-NET 1

source_name: moDC derived from monocytes of healthy donor 1 cultivated with T1D NETs


title: RNA-seq_Bcat_Cultured_R4

data_processing:
Salmon version 0.14.0 (Patro et al., 2017) was used to quantify expression of transcripts from RNA-seq experiments using GENCODE release M21 (salmon quant -l A –validateMappings –mimicStrictBT2 --rangeFactorizationBins 4 --incompatPrior 0.0 --useVBOpt --seqBias --gcBias --posBias --biasSpeedSamp 10). To visualize RNA-seq data on an IGV browser (Robinson et al., 2011; Thorvaldsdóttir et al., 2013), HISAT2 version 2.1.0 (Kim et al., 2015) was used to generate alignment bam files (hisat2 --dta) and then deepTools was used to generate bigwig files (bamCoverage -bs 1 --normalizeUsing CPM).
Genome_build: mm10

extract_protocol:
For cultured ECs, RNA was extracted by adding QIAGEN Buffer RLT Plus directly into the well followed by extraction using the RNeasy Micro Plus kit.
WT cultured brain EC RNA-seq libraries for replicates one, two, five, and six and beta-catenin stabilized brain EC RNA-seq libraries for all four replicates were paired-end sequenced for 36 cycles on a NextSeq500.


title: RNA-seq_Bcat_Cultured_R3


title: RNA-seq_WT_Cultured_R6


title: RNA-seq_Bcat_Cultured_R1


title: RNA-seq_WT_Cultured_R4

extract_protocol:
For cultured ECs, RNA was extracted by adding QIAGEN Buffer RLT Plus directly into the well followed by extraction using the RNeasy Micro Plus kit.
WT cultured brain EC RNA-seq libraries for replicates three and four were prepared by Omega Bioservices (Georgia) and paired-end sequenced for 150 cycles. Sequencing libraries that contained overrepresented adaptor sequences were trimmed using Trim Galore (https://github.com/FelixKrueger/TrimGalore).


title: RNA-seq_Bcat_Cultured_R2


title: RNA-seq_WT_Cultured_R3


title: RNA-seq_WT_Cultured_R1


title: RNA-seq_WT_Cultured_R5


title: RNA-seq_Adult_Brain_GFPpos_R2

extract_protocol:
For acutely isolated ECs, RNA was extracted from GFP-positive and GFP-negative cells that were FACS sorted directly into QIAGEN Buffer RLT Plus and then processed using the RNeasy Micro Plus kit (74034, QIAGEN, Venlo, Netherlands).
For RNA-seq, total RNA was converted to cDNA and amplified (Ovation Ultralow System V2-32, 0342HV, NuGEN Technologies, San Carlos, CA). Amplified cDNA was fragmented, end-repaired, linker-adapted, and single-end sequenced for 75 cycles on a NextSeq500 (Illumina Inc.). Cultured brain EC RNA-seq libraries were paired-end sequenced for 36 cycles on a NextSeq500.


title: LysoDC

city: Marseille

first: Hugues

last: Lelouard

address: parc Scientifique de Luminy case 906

country: France

institute: CIML CNRS UMR 7280

description: 23,000 LysoDC were isolated from 246 Peyer's patches from 35 C57BL/6Rj mice and processed using the Chromium Single Cell 3’ kit from 10X genomics (California, USA) for the library preparation and the NextSeq 500/550 High Output Kit v2 (75 cycles) cartridges from Illumina for the sequencing. FASTQ raw files were processed using Cell Ranger software (v2.1.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads were aligned to the mouse mm10 genome.

data_processing:
FASTQ raw files were processed using Cell Ranger software (v2.1.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads   were aligned to the mouse mm10 genome.
Quality control (QC) was performed to remove poor quality cells thanks to in-house developed R scripts using Seurat v2 R package.
Expression data were normalized using the Seurat R package NormalizeData function (using logNormalize method and scale factor of 10000).
Expression data were centered and regressed from the number of UMI factor using the Seurat R package ScaleData function (centering true and scaling false).
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: csv, tsv and mtx files

source_name: Peyer's patch

extract_protocol:
PP  from 35 C57BL/6Rj  mice were digested for 40 min at room temperature with collagenase/DNase . All subsequent procedures were at 0–4°C. CD11c+ cells were enriched using anti-CD11c microbeads and an AutoMACS magnetic cell separator according to manufacturer’s instructions. CD11c+ cells were preincubated on ice for 10 min with 2.4G2 antibody to block Fc receptors and stained for the  surface markers CD11c, MHCII, SIRPa, Bst2, CD4, CD11b, XCR1 and CD24. Cell viability was evaluated using LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit (Life Technologies). Live LysoDC were sorted using a  FACSAria III and processed according to the ChromiumTM Single Cell 3’ Reagent Guidelines from 10X genomics.
RNA library was prepared by the NGS facility (HalioDx) using the Chromium Single Cell 3’ kit protocol from 10X genomics (California, USA)

tag: mouse strain

value: Peyer's patches (n=246)

tag: mouse age

value: 8 weeks


title: RNA-seq_Adult_Brain_GFPpos_R1


title: RNA-seq_Adult_Brain_GFPneg_R2

source_name: Adult GFP-negative sorted cells from brain

value: Non-endothelial


title: ATAC-seq_Adult_Brain_GFPpos_R1


title: RNA-seq_Adult_Brain_GFPneg_R1


title: RNA-seq_Adult_Cerebrum_GFPpos_R2

source_name: Adult GFP-negative sorted cells from cerebrum


title: RNA-seq_Adult_Cerebrum_GFPpos_R1


title: RNA-seq_Adult_Cerebrum_GFPneg_R2


title: RNA-seq_Adult_Cerebrum_GFPneg_R1


title: 24-BLIMP1-TFR4

first: Alexander

last: Dent

address: 950 W. Walnut St. R2 302, Walther Oncology Center

institute: Alexander Dent

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC mm10
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

source_name: BLIMP1_TFR cells

extract_protocol:
Total RNA was collected from freshly sorted TFR cells using the RNeasy Plus Micro kit (QIAGEN) and subjected to RNA-seq
KAPA mRNA Hyperprep Kit

tag: genotype/variation

value: Blimp1-flox (Blimp1) Foxp3-cre

value: 2x oral challenge with peanut + cholera toxin

value: spleen

value: CD4+ T cells

tag: cell subtype

value: freshly sorted TFR cells


title: UNTR_PolIISer5_rep2

description: ChIP-Seq

value: Vehicle

value: Abcam Ab5131


title: RNA-seq_WT_Cultured_R2

tag: age


title: 23-BLIMP1-TFR3


title: 22-BLIMP1-TFR2


title: 20-WT-TFR4

source_name: WT_TFR cells

value: Wildtype (WT)


title: 21-BLIMP1-TFR1


title: E14_Input_22

city: Farmington

first: Chia-Lin

last: Wei

state: CT

address: 10 Discovery Drive

department: Genome Technologies

institute: The Jackson Laboratory

data_processing:
Raw reads were quality trimmed along with the adapter using cutadapt v1.14  (options: -e 0.2 -a AGATCGGAAGAGC --minimum-length 20 --trim-n -n 3). The trimmed-reads were mapped on the mm10 genome using BWA v0.7.12  (options: aln –l 25 followed by samse). Only the de-duplicated uniquely mapped reads were used for downstream analysis.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

source_name: Mouse embryonic stem cells

growth_protocol: ES E14 were cultured routinely under feeder-free conditions on 0.1% gelatin coated dishes in Knockout DMEM supplemented with 15% FBS, 2 mM L-glutamine , 0.1 mM non-essential amino acids, 100 U/ml Penicillin/Streptomycin, 0.05 mM 2-mercaptoethanol, 1,000 U/ml ESGRO mouse LIF Medium Supplement (Leukemia Inhibitory Factor) and maintained at 37ºC with 5% CO2.

extract_protocol:
Cells were lysed using SDS-based lysis buffer and sonicated, protein-DNA complexes were then isolated with antibody.
Immunoprecipitated protein-DNA complex were ligated with illumina-compatible adaptors, amplified by PCR and sequenced.

value: E14 cell line

value: embryonic stem cells

tag: ip antibody


title: 19-WT-TFR3


title: E14_Input_21

tag: cell line


title: E14_Input_23


title: HCT116-PRMT1-S23

city: Nanjing

first: Bing

last: Yao

state: Jiangsu

address: Longmian Road 101

department: Department of Medical Genetics

institute: Nanjing Medical University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version13.1,Agilent Technologies)were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs.

label: total RNA

label_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: The HCT116 cells were purchased from the Shanghai Institute of Cell Biology, Chinese Academy of Sciences (Shanghai, China). Cells were maintained at 37C in a humidified air atmosphere containing 5% carbon dioxide in McCOY's 5A medium supplemented with 10% FBS (Invitrogen).

extract_protocol: Total RNA fromcultured cells was extracted using TRIzol reagent (Invitrogen). cDNAs were synthesized with a HiScript 1st Strand cDNA Synthesis Kit (Vazyme Biotech, China).

treatment_protocol: SiRNA against PRMT1 was synthesized by Jima. The sequences used were: PRMT1 siRNA-1, 5’-CUGAAGUCCAGGUCGAUGGUGAAGUC-3’; PRMT1 siRNA-2, 5’-UUGUAGUCUUUGUACUGCC-3’. HCT116 cells were transfected with oligonucleotides or indicated constructs using Lipofectamine 3000 (Invitrogen) according to the manufacturer's instructions.

value: HCT116 cells

value: colorectal cancer cells


title: CA1_Pyr_FACS_1

city: Cambridge

first: Kirsty

last: Sawicka

address: Robinson Way

department: University of Cambridge

institute: CRUK Cambridge Insititute

description:
PolyA RNA
processed data file: featureCounts_CA1_Pyr_FACS.txt

data_processing:
Alignment with STAR to mm10 genome.
Read counts per gene with featureCounts and GENCODE annotation.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: featureCounts_CA1_Pyr_FACS.txt: Tab-delimited text file

source_name: FACS-purified TdTomato-positive CA1 pyramidal neurons

growth_protocol: Hippocampal tissue from postnatal day 28-32 male mice.

extract_protocol:
Trizol RNA extraction followed by DNase I treatment and further purification using the RNeasy minelute cleanup kit (Qiagen).
Poly(A) RNA selection followed by Illumina TruSeq RNA library preparation.

treatment_protocol: Hippocampal tissue was digested with papain and triturated to obtain a single cell suspension. Live, tdTomato positive cells were separated on a BD FACSAria Cell Sorter.

tag: genotype

tag: strain/background

value: CA1 pyramidal neurons

value: male

value: postnatal day 28-32


title: HCT116-SMARCA4-S23

treatment_protocol: SiRNA against SMARCA4 was synthesized by Jima. The sequences used were: SMARCA4 siRNA-1, 5’-UCGCUUUGGUUCGCAAAUC-3’; SMARCA4 siRNA-2, 5’-UUCCUCCUCAUUCAGGUCC-3’. HCT116 cells were transfected with oligonucleotides or indicated constructs using Lipofectamine 3000 (Invitrogen) according to the manufacturer's instructions.


title: CA1_Pyr_FACS_2


title: HA MRSA (nm)_E_rep3

city: Brisbane

first: Imalka

middle: U P K

last: Tennakoon

state: QLD

address: 60,Musk Avenue,Kelvingrove

department: Institute of Health and Biomedical Innovation

country: Australia

institute: Queensland University of Technology

description:
Total RNA
Processed_Data_N315AsReference_E.xlsx, Processed_Data_USA300AsReference_E.xlsx

data_processing:
Adapter sequence trimmed data in FASTA format was exported to CLC Genomics Workbench Version 6.2.2 software.
Data quality was checked and trimmed using length (Maximum length: 200 bp and minimum length: 50 bp) and PHRED score (Reads with PHRED quality score less than 16 were excluded).
RNA-seq experiments were set up in CLC Genomics workbench software using the two references and the resulting data was normalized by count
Genome_build: two reference genomes used for analysis USA300_FPR3757 (NCBI RefSeq accession numbers NC_007793.1, NC_007790.1, NC_007791.1, NC_007792.1) and N315 strains (NCBI RefSeq accession numbers NC_002745.2, NC_003140.1)
Supplementary_files_format_and_content: Excel sheets with RPKM values included for each samples

organism: Staphylococcus aureus

source_name: bacteria

growth_protocol: overnight culture of S.aureus, diluted 1:10 and grown in fresh Brain Heart infusion Broth at 370C.    Total RNA extracted during Stationary growth phase (OD600=1.0) and exponential growth phase (OD600=0.5)

extract_protocol:
Total RNA was extracted with “RNeasy mini kit” (Qiagen) with additional “on-column DNase digestion”,mRNA enrichment/rRNA depletion was done using Ribo-Zero™ Magnetic Kit (Gram-Positive Bacteria) (epicentre, an Illumina company)
libraries constructed as per “Ion Total RNA-seq Kit V2” (Ion Torrrent, Life Technologies)

treatment_protocol: No treatments were applied.

tag: clonal complex

tag: growth phase

value: Exponential

tag: strain

value: clinical


title: CA1_Pyr_FACS_3


title: HCT116-PRMT1-NC

tag: treatment


title: HCT116-SMARCA4-NC


title: HA MRSA (nm)_E_rep2


title: 18-WT-TFR2

city: Indianapolis


title: E14_Input_20


title: 17-WT-TFR1


title: HA MRSA (m)_E_rep3


title: HA MRSA (nm)_E_rep1


title: E14_Input_19


title: HA MRSA (m)_E_rep2


title: HA MRSA (m)_E_rep1


title: B6NJ_si_chr2_G5_RNA-seq_rep3

data_processing:
Raw reads were trimmed with Trim Galore v0.4.0 (options: -q 30 -e .20 --length 15). Trimmed reads were mapped to mm10 genome with hisat2 v2.1.0 (options: --dta-cufflinks -x)
Genes expression were computed by HTSeq v0.6.1 (options: -s=reverse –nonunique=all) for all gene models in gencode.vm14.grcm38 excluding those known as not transcribed by RNA polymerase II like pseudogenes, snoRNA, snRNA, miscRNA and riboRNA.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

growth_protocol: ES B6NJ and its derivative KO lines were cultured rountined on irradiated MEF-feeder layer with high glucose DMEM supplemented with 15% ES Cell FBS, 1X non-essential amino acids, 1X Glutamax, 100 U/ml Penicillin/Streptomycin, 1mM sodium pyruvate, 0.1mM 2-mercaptoethanol and further supplemented with PD0325901 and CHIR99021.

extract_protocol: RNA-seq libraries were prepared using illumina Truseq mRNA stranded protocol following manufacturer's instructions.

value: B6NJ derived KO cells

tag: clone


title: CA MRSA (PVL-)_E_rep3


title: HCT116-SMARCA4-S12


title: B6NJ_si_chr2_G5_RNA-seq_rep2


title: E14_Input_18


title: E14_Input_16


title: HCT116-PRMT1-S12


title: UNTR_Input_all_reps

description: ChIP-Seq

value: breast cancer cells

tag: chip antibody

value: none (input)


title: CA MRSA (PVL-)_E_rep2


title: B6NJ_si_chr2_G5_RNA-seq_rep1


title: CA MRSA (PVL-)_E_rep1


title: CA MRSA (PVL+)_E_rep2


title: B6NJ_si_chr2_D10_RNA-seq_rep3


title: CA MRSA (PVL+)_E_rep1


title: E14_Input_12


title: E14_Input_14


title: CA MRSA (PVL+)_E_rep3


title: E14_Input_11


title: CA MRSA (PVL-)_S_rep2

description:
Total RNA
Processed_Data_N315AsReference_S.xlsx, Processed_Data_USA300AsReference_S.xlsx

value: Stationary


title: HA MRSA (m)_S_rep1


title: B6NJ_si_chr2_D10_RNA-seq_rep1


title: B6NJ_si_chr3_H7_RNA-seq_rep3


title: CA MRSA (PVL-)_S_rep1


title: UNTR_PolIISer2_rep2

description: ChIP-Seq

tag: chip antibody info.

value: Abcam Ab5095


title: CA MRSA (PVL+)_S_rep2


title: MG4H_PolII8WG16_rep1

description: ChIP-Seq

tag: cell type

value: Santa Cruz Biotechnology Sc-56767


title: E14_Input_10


title: B6NJ_si_chr3_H7_RNA-seq_rep2


title: E14_Input_6


title: B6NJ_si_chr3_H7_RNA-seq_rep1

data_processing:
Raw reads were trimmed with Trim Galore v0.4.0 (options: -q 30 -e .20 --length 15). Trimmed reads were mapped to mm10 genome with hisat2 v2.1.0 (options: --dta-cufflinks -x).
Genes expression were computed by HTSeq v0.6.1 (options: -s=reverse –nonunique=all) for all gene models in gencode.vm14.grcm38 excluding those known as not transcribed by RNA polymerase II like pseudogenes, snoRNA, snRNA, miscRNA and riboRNA
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10


title: E14_Input_13


title: HA MRSA (nm)_S_rep2


title: B6NJ_si_chr2_D10_RNA-seq_rep2


title: HA MRSA (nm)_S_rep1


title: Nup93.rep2

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Sequencing reads were aligned to genome assembly dm3 using Bowtie2 (version 2.2.9) with default parameters and “--local” to allow soft clipping of ends.
Alignments were further processed by SAMtools (version 0.1.19) to remove low quality alignments (“-q 10”), PCR duplicates (“rmdup -s”) and mitochondrial reads.
Reads that passed filter were used to call peaks with MACS2 (v2.1.0, “--qvalue 0.05 --mfold 2 50 --broad”).
Peaks that overlapped between biological replicates were retained for each antibody.
For visualization, each individual library was normalized to 10 million reads per library and then track for each library subtracting its corresponding IgG control was generated using BEDtools (“genomecov”) and Deeptools (“bigwigCompare –ratio=subtract --binSize=10”).
BigWig files were then converted from bedGraph files using command "bedGraphToBigWig".
Genome_build: dm3 (BDGP Release 5)
Supplementary_files_format_and_content: BedGraph files were generated for each library using Bedtools 'genomecov' with scale normalized to 10 million reads per library. IgG were then subtracted from IP bedGraph files using Deeptools 'bigwigCompare'. BigWig files were converted from bedGraph files.

organism: Drosophila melanogaster

source_name: embryonic cells

extract_protocol:
Lysates from embryonic cells were clarified from sonicated nuclei and Nup-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Illumina's instructions.

value: Embryonic cells

value: wild type

value: Nup93 (Pascual-Garcia et al., 2017)


title: S2-Input

description: control for S2 libraries

data_processing:
Sequencing reads were aligned to genome assembly dm3 using Bowtie2 (version 2.2.9) with default parameters and “--local” to allow soft clipping of ends.
Alignments were further processed by SAMtools (version 0.1.19) to remove low quality alignments (“-q 10”), PCR duplicates (“rmdup -s”) and mitochondrial reads.
For visualization, each individual library was normalized to 10 million reads per library and then track for each library subtracting its corresponding Input control was generated using BEDtools (“genomecov”) and Deeptools (“bigwigCompare –ratio=subtract --binSize=10”).
BigWig files were then converted from bedgraph files using command "bedGraphToBigWig".
Genome_build: dm3
Supplementary_files_format_and_content: Bedgraph files were generated for each library using Bedtools 'genomecov' with scale normalized to 10 million reads per library. IgG were then subtracted from IP bedgraph files using Deeptools 'bigwigCompare'. Bigwig files were converted from bedgraph files.

extract_protocol:
Lysates from embryonic cells or 3rd instar brains were clarified from sonicated nuclei and lamin-DNA complexes were isolated with specific antibody
Libraries were prepared according to Illumina's instructions for HiSeq 2000 for KC or S2 cells and NextSeq 500/550 High Output Kit when brains were analyzed.


title: HA MRSA (m)_S_rep2


title: B6NJ_si_chr3_C2_RNA-seq_rep2

data_processing:
Raw reads were trimmed with Trim Galore v0.4.0 (options: -q 30 -e .20 --length 15). Trimmed reads were mapped to mm10 genome with hisat2 v2.1.0 (options: --dta-cufflinks -x).
Genes expression were computed by HTSeq v0.6.1 (options: -s=reverse –nonunique=all) for all gene models in gencode.vm14.grcm38 excluding those known as not transcribed by RNA polymerase II like pseudogenes, snoRNA, snRNA, miscRNA and riboRNA.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10


title: Nup93.rep1


title: Nup107.rep1

value: Nup107 (this study)


title: B6NJ_si_chr3_C2_RNA-seq_rep1

data_processing:
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10


title: IgG.forNup107

description: Control for Nup107 libraries.

value: IgG (rabbit)


title: CA MRSA (PVL+)_S_ rep1


title: IgG.forElysNup93

description: Control for Elys and Nup93 libraries.


title: Elys.rep1

value: Elys (Pascual-Garcia et al., 2017)


title: Elys.rep2


title: CTCF_ChIP_rep1

description:
CTCF_ChIP_treat.bigWig
CTCF_ChIP_foldEnrich.bigWig
CTCF_ChIP.narrowPeak.gz

data_processing:
Raw reads were quality trimmed along with the adapter using cutadapt v1.14  (options: -e 0.2 -a AGATCGGAAGAGC --minimum-length 20 --trim-n -n 3). The trimmed-reads were mapped on the mm10 genome using BWA v0.7.12  (options: aln –l 25 followed by samse). Only the de-duplicated uniquely mapped reads were used for downstream analysis.
Peak calling was performed on the pair of ChIP and input dataset with MACS v2.1.1.20160309 (options: --nomodel --extsize 250 -B –SPMR -g mm ; broad peak additional options: --broad --broad-cutoff 0.1). bedGraphToBigWig from kentUtils was used to convert MACS2 generated bedgraph to bigWig format. Fold enrichment was computed with MACS2 bdgcmp and the output bedgraph file was converted to bigWig with bedGraphToBigWig.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

value: E14 cell line

value: embryonic stem cells

value: CTCF (Abcam ab70303)


title: S2-L7-rep2

value: lamin L7 antibody


title: asESCs.WGBS.r3

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

description: bisulfite treated  genomic DNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove adaptor sequences and low quality bases;
For whole genome bisulfite sequencing (WGBS), the clean reads were first mapped to mouse reference genome mm10 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; while for RNA-seq, the cleaned reads were aligned to the mouse mm10 reference genome using Tophat (v2.0.12) with default settings (Trapnell et al., 2009).
For WGBS, methylation level of covered cytosines, including CpG, CHH and CHG were estimated using comstomized perl scripts; while for RNA-seq, HTSeq (0.6.1) was used to do the reads counting and then gene expression level was calculated using the RPKM method (Reads Per Kilobase transcriptome per million reads).
Genome_build: mm10
Supplementary_files_format_and_content: Methylation calling txt files include the methylation level of covered cytosines, including CpG, CHH and CHG context; while gene RPKM txt files include the RPKM values of RefSeq genes.

extract_protocol:
The isolated genomic DNA were used to construct the WGBS library, as previously described (Zhang et al., 2017). RNA-seq were performed under the instruction of mRNA library construction kit (NEB).
Total RNA were extracted from approximately one million to two million cells using RNeasy Mini Kit (QIAGEN) according to the recommendation of manufacturer and then NEBNext® Poly(A) mRNA Magnetic Isolation Module was used to isolate mRNA from total RNA. Using mRNA as input, the first and second strand cDNAs were synthesized by NEBNext® RNA First Strand Synthesis Module and NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module, respectively. Final libraries were prepared using KAPA Hyper Prep Kits (8 PCR cycles) and sequenced on HiSeq4000 platform. Following the manufacturer’s instructions, genomic DNA was extracted from stem cells using the DNeasy Blood & Tissue Kit (Qiagen). Remaining RNA was removed by treating with RNase A. Three replicated samples from each of these stem cells were used for library preparation to ensure repeatability of experiment. In short, 2 μg of genomic DNA spiked with 10 ng of lambda DNA were fragmented to about 300 bp with Covaris S220. Next, end repair and A-ligation were performed to the DNA fragments. Methylated Adaptor (NEB) was then ligated to the DNA fragments. In order to reach >99% bisulfite conversion, the adaptor-ligated DNA was treated twice using EZ-96 DNA Methylation-Direct™ MagPrep (Zymo Research). The resulting single-strand DNA fragments were amplified by 4 PCR cycles using the KAPA HiFi HotStart Uracil+ ReadyMix (2×). At last, the libraries were sequenced on HiSeq4000 platform to generate 150-bp paired-end reads.

value: Embryonic stem cell

tag: passages

value: asESCs


title: S2-L7-rep1


title: asESCs.WGBS.r2

description: bisulfite treated  genomic DNA


title: B6NJ_si_chr3_C2_RNA-seq_rep3

value: B6NJ derived KO cells


title: asESCs.WGBS.r1

description: bisulfite treated  genomic DNA


title: RNApolII_chiapet_rep2

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) v0.0.1a (https://github.com/cheehongsg/CPU). CPU (options: tag -W) removed the adaptors, and extracted the intra-molecular and inter-molecular paired tags based on the linker sequence identified in the read and the remaining read-pairs without linker sequence. Tags (>=18bp) and reads without linker sequence were mapped to mouse genome (mm10) independently  using CPU (options: memaln -T 15), which utilized BWA (options: aln and mem) according to the tag/read length. CPU (options: pair) further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration. Next, deduplication of uniquely-mapped pair-end tags/reads arising from clonal PCR amplification was performed with CPU (options: dedup).
The non-redundant uniquely-mapped pair-end tags are merged with samtools and deduplicated with CPU (options: dedup), producing a single RNA PolII alignment file. RNA PolII binding peaks were called with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B –SPMR -g mm) where the single RNA PolII alignment file is specified as the treatment file and the combined 28 input files (23 E14_input, 2 CTCF ChIP input, 2 H3K27me3 ChIP input and RNAPolII_ChIP_r1_input) as the input control.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

extract_protocol:
Cells were lysed using SDS-based lysis buffer and sonicated, protein-DNA complexes were then isolated with antibody.
Immunoprecipitated protein-DNA complex were ligated with linkers. The proximity ligated chromatin complex was eluted with 1% SDS and de-crosslinked using proteinase K and purified. The purified fragments were tagmented using the Nextera DNA Sample Preparation Kit (Illumina). The linker ligated ChIA-PET constructs were selected using streptavidin magnetic beads. The magnetic beads were blocked with yeast tRNA prior to the selection. The streptavidin selected constructs were amplified with PCR and purified.

value: RNA polymerase II clone (Covance MMS126R-500)


title: E14_Input_5


title: E14_RNA-seq_rep2

data_processing:
Raw reads were trimmed with cutadapt v1.14 (options: -e .20 -q 30 --minimum-length 20 --trim-n  -a AGATCGGAAGAGC -A AGATCGGAAGAGC). Trimmed reads were mapped to mm10 genome with HiSat2 v2.1.0 (options: --rna-strandness FR --dta-cufflinks).
Gene expression was computed with Cufflinks v2.2.1 (options: -u --seed 1122334455 --library-type fr-firststrand) for all gene models in gencode.vm14.grcm38 primary assembly excluding rRNA, and those on ChrM and unplaced contigs.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

extract_protocol:
Total RNA was extracted from cell pellets using Trizol reagent followed by a purification with Qiagen RNeasy column.
RNA-seq libraries were prepared using illumina Truseq mRNA stranded protocol following manufacturer's instructions.


city: Burnaby

first: David

last: Vocadlo

state: British Columbia

address: 8888 University Drive

department: Chemistry

country: Canada

institute: Simon Fraser University

description:
ogako-OGA-ChIP-seq
processed data file: OGA-ChIP-seq-peaks.bed
OGA ChIP-seq in OGA knockout Drosophila larvae

data_processing:
O-GlcNAc-seq: FASTQ sequencing files were aligned to a concatenated reference genome of D. melanogaster (dm3), S. cerevisiae (sacCer3), and the three synthetic gBlock fragments using the snap-aligner single command from SNAP version 1.0beta.18. The yeast chromosomes were re-name with the prefix "yeast" to avoid conflicts with the same chromosome names as Drosophila.
O-GlcNAc-seq: The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a
O-GlcNAc-seq: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0. Yeast spike-in normalized BDG files were generated by multiplying by the fourth column, which specifies the sequencing coverage, of the BDG file by the normalization constants. These normalization constants were calculated by dividing the number of base pairs that aligned to the sacCer3 genome from the time point that had the least sacCer3 aligned base pairs by the number of base pairs that aligned to the sacCer3 reference genome from each time point. This was done within each replicate separately. The command awk -F'\t' '{$4=$4*a;print}' a=NF OFS='\t' <$.bdg> was used to do this, where NF is the normalization factor, which are specified in Table 1, and <$.bdg> is the appropriate time course input BDG file.
O-GlcNAc-seq: Peaks were called by calculating the coordinates that contained 5 times the average base pair sequencing coverage within each time course experiment. This was done for the no feed controls as well. The coordinates of base pairs that satisfied this requirement were then merged if they were within 30 base pairs of each other. This was done with the command awk '{ if( $4 > 5X) print}' <$.bdg> | cut -f 1,2,3 | bedtools merge -d 30, where 5X indicates 5 times the average base pair sequencing coverage within each time course experiment and <$.bdg> indicates the appropriate time course BDG file. For each time point, the peaks that occurred from the no feed controls were eliminated from the time course experiment peaks using the bedtools intersect -v command. This effectively removed false positives from the analysis. Peaks resulting from the intersection of replicate time points were kept using the regular bedtools intersect command. Peaks at time point 0 for WT and OGA-null were then intersected using the bedtools intersect command. Peaks that were less than 20 base pairs were then expanded from their midpoint by 10 base pairs on each side to a peak length of 20 base pairs. This strategy resulted in 1883 peaks and enabled focus on coordinates that consistently contained O-GlcNAz peaks within both WT and OGA-null and each replicate.
O-GlcNAc-seq pilot study: FASTQ sequencing files were aligned to the D. melanogaster (dm3) genome using the snap-aligner single command from SNAP version 1.0beta.18.
O-GlcNAc-seq pilot study: The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a
O-GlcNAc-seq pilot study: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0.
OGA ChIP-seq: Fastq files were aligned to the dm3 genome the Burrows–Wheeler Aligner version 0.7.5a-r405 algorithm. The resulting BAM-format alignment files were sorted, cleared of duplicates and indexed using the SAMtools commands sort, rmdup -s, and index, respectively, using SAMtools version 0.1.19-96b5f2294a.
OGA ChIP-seq: BDG files were generated from the BAM files using the command bedtools genomecov -ibam -bg command using bedtools v2.17.0.
OGA ChIP-seq: Peaks were called by calculating the coordinates that contained 5 times the average base pair sequencing coverage within both OGA ChIP-seq experiments (WT and OGA-null). Peaks within the OGA-null experiment were considered false positives and were subtracted from the peaks called in the WT experiment using the bedtools intersect -v command to yield the final OGA ChIP-seq peaks.
Genome_build: dm3, sacCer3 and synthetic DNA probes.
Supplementary_files_format_and_content: Bdg files and bed files containing ChIP-seq and O-GlcNAc-seq loci. Bed files of O-GlcNAc-seq data contain normalized sequencing depth at each O-GlcNAc bearing locus accross time points for WT and OGA-null replicates.

source_name: OGA ChIP-seq_OGA knockout larvae

extract_protocol:
50 larvae were cross-linked in 5% formaldehyde in PBS with 0.5% Triton X-100 (0.5% PBST) for 5 min by vortexing occasionally at room temperature. The flies were then washed three times in 0.1% PBST, using the five volumes as used for fixing. and glycine was added to a final concentration of 0.125 M. The samples were washed once with PBS, 1 mM PMSF, protease inhibitor cocktail (Roche) followed by two washes in PBS, 1 mM PMSF and protease inhibitor cocktail. These flies were homogenized in 500 μl Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1). To ensure shearing of the cross-linked DNA into 200-500 bp long fragments, 120 μl glass beads were added prior to sonication for 4 min using a sonicator (Sonic Dismembrator Model 500, Fisher Scientific) at high setting (30 s ON, 30 s OFF). The samples were cleared by centrifuging for 10 min at 14,000 x g at 4 °C. For each ChIP (WT and OGA-null), 150 μl of cell lysate was diluted by a factor of ten in ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl), and protein inhibitors were added. To reduce nonspecific background the diluted lysate was pre-cleared by incubation with 60 μl of equilibrated Dynabeads Protein A (Thermo Fisher Scientific) for 30 min at 4 °C with agitation. For immunoprecipitation, the cleared lysates were incubated with 5 μl of normal rabbit IgG (Control; Santa Cruz, sc-2027) and rabbit antibodies (MEGA5, Proteintech #14711-1-AP) raised against full-length Drosophila OGA protein overnight at 4 °C on a rotating platform. The antibody complexes were precipitated by incubation with equilibrated Protein A Dynabeads for 1 h at 4 °C. The beads were washed for 4 min with agitation at 4 °C with the following buffers; once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl pH 8.0, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl pH 8.0, 500 mM NaCl), once with LiCl-containing buffer (250 mM LiCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate), and twice with TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The protein/DNA complexes were eluted from the antibody by incubating for 15 min at room temperature in 250 μl Elution buffer (1% SDS, 0.1 M NaHCO3) with rotation. The elution was repeated once, and the eluates were combined to a total volume of 500 μl. NaCl was added to a final concentration of 200 mM, and protein/DNA crosslinks were reversed by heating at 65 °C for 4 h. A total of 10 μl of 0.5 M EDTA, 20 μl of 1 M Tris-HCl pH 6.5, and 1 μl of 20 mg/ml proteinase K were added before an additional incubation at 45 °C for 1 h. The DNA was recovered by phenol/chloroform extraction followed by ethanol precipitation. The immunoprecipitated DNA was then dissolved in 24 μl water.
The libraries were prepared according to the manufacturer’s instructions using the NEBNext kit (E6200). Briefly, DNA was fragmented by sonication to a maximum of 300 bp. Next, the ends of the fragments were repaired with a combination of fill-in reactions and exonuclease activity to produce blunt ends that were then tailed with an A-base. Illumina-specific adaptors were ligated followed by removal of unligated adaptors using AMpure XP beads (Beckman Coulter). Finally, a PCR with 12-15 cycles for both kits was performed to enrich final adaptor-ligated fragments. Quality and quantity were assessed on High Sensitivity dsDNA Agilent Bioanalyzer Chips and Quibit. WT and OGA-null O-GlcNAc-seq libraries and OGA ChIP-seq libraries were sequenced on the Illumina NextSeq 500 High Output (75 cycles, 400M reads) platform. The additional replicates for both WT and OGA-null DMSO control from an earlier pilot study were sequenced on the MiSeq platform, using v3, 150-cycle reagent kits (Illumina).

treatment_protocol: Drosophila were grown at 25°C on cornmeal-molasses-yeast medium supplemented with the mold inhibitors tegosept and propionic acid.

tag: strain background

value: Oregon R

value: OGA knockout

tag: stage/tissue

value: larvae

tag: chip strategy

value: Lysates were clarified from sonicated nuclei and OGA/DNA complexes were isolated with MEGA5 antibody (Proteintech #14711-1-AP). Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 5592-5597.


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 36h growth on DMSO media

description:
ogako.r2_36
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 36h growth on DMSO media

source_name: O-GlcNAc-seq_OGA KO larvae_150uM GalNAz media for 36h followed by 36h growth on DMSO media

extract_protocol:
The larvae were collected and rinsed with PBST (PBS + 0.1% Triton X-100) three times to remove adhering corn food. One volume of hexanes (a mixture of isomers) was equilibrated for 30 min against 0.175 vol of 37% formaldehyde and 0.130 vol of 10X PBS (1.37 M NaCl, 27 mM KCl, 43 mM Na2HPO4 and 14 mM KH2PO4), pH 7.5, to make the mixture 5% formaldehyde and 1X PBS. Only the upper organic phase was used for crosslinking. Larvae were fixed in 10 ml of buffered 5% formaldehyde/hexanes per gram of larvae by vigorous shaking for 5 min at room temperature. The larvae were allowed to settle, and the formaldehyde/hexanes solution was removed by centrifugation (3,000 x g for 5 min at RT). The larvae were washed twice in a solution containing 1X PBS and 0.5% Triton X- 100 (0.5% PBST), using the five volumes as used for fixing. They were then stored at -80°C. Chromatin was purified by quickly thawing frozen larvae and resuspending them in buffer A [0.3 M sucrose, 15 mM NaCl, 5 mM MgCl2, 15 mM Tris pH 7.5, 60 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 0.5 mM dithiothreitol (DTT) and 1 mM phenylmethylsulfonyl fluoride (PMSF)]. They were homogenized with 20-25 strokes of a hand-held type B Dounce homogenizer. Triton X-100 was added to 0.3%, and the homogenate was centrifuged (2,000 x g for 15 min at 4°C). The pellet was resuspended in buffer B (100 mM NaCl, 10 mM Tris pH 7.9, 1 mM EDTA, 0.1% v/v NP-40 and 1 mM PMSF) and homogenized with ~5 strokes of a hand-held type B Dounce homogenizer. The homogenate was then sheared by 20 cycles (20 × 20 s on and 50 s off cycles, 40% power settings) through a sonicator (Sonic Dismembrator Model 500, Fisher Scientific) to an average size of ~200 to 700 bp chromatin fragments. After sonication, debris was removed by centrifugation at 4°C for 10 min at 13,000 r.p.m., and an equal amount of 6 M urea was added to the solution and then incubated for 10 min at 4°C on a rotating wheel. The soluble chromatin was dialyzed using a membrane with a molecular weight cut-off of 3.5 kDa, at 4°C against 2 L dialysis buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 4% glycerol) overnight. Insoluble debris was removed by quick centrifugation (7,500 r.p.m., 2 min). The chromatin solution was pre-cleared with 100 μl Streptavidin-agarose slurry (Sigma) beads for O-GlcNAz modified or vehicle-only chromatin separately and incubated for 1 hour at 4°C on a rotating wheel. The pre-cleared chromatin was aliquoted after centrifugation at 4°C for 2 min at 7,500 r.p.m., snap-frozen in liquid nitrogen and stored at −80°C for future use. For click chemistry, 20-50 μg chromatin DNA was incubated with iodoacetamide (IAA) to a final concentration of 15 mM, agitate mildly for 30 min at RT then added DMSO solution of dibenzylcyclooctyne-S-S-PEG3-Biotin (DBCO-S-S-PEG3-Biotin, Jena Bioscience GmbH) to a final concentration of 40 μM. The samples were protected from light and agitated mildly for 1 hour at RT. The unreacted probe was filtered off by the Amicon Ultra-0.5 mL centrifugal filter (15K cut-off) (EMD Millipore). Biotinylated-probe-chromatin complexes were captured by incubation with 50 μl Streptavidin magnetic beads (NEB) at 4°C for 2 hours. Beads were washed with 0.5 ml of the following buffers: three washes with low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), followed by three washes with high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), then three washes with lithium wash buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0); then two washes with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were resuspended in 100 μl TE containing 0.5% SDS, 15 mM DTT and incubated with 0.15 mg/ml proteinase K at 55°C for 3-4 hours. DNA-protein complex was de-crosslinked by incubating overnight at 65°C (not more than 15 hours). ChIP-DNA was purified with QIAquick PCR Purification Kit and stored at -20°C.
The libraries were prepared according to the manufacturer’s instructions using the NEBNext kit (E6200). Briefly, DNA was fragmented by sonication to a maximum of 300 bp. Next, the ends of the fragments were repaired with a combination of fill-in reactions and exonuclease activity to produce blunt ends that were then tailed with an A-base. Illumina-specific adaptors were ligated followed by removal of unligated adaptors using AMpure XP beads (Beckman Coulter). Finally, a PCR with 12-15 cycles for both kits was performed to enrich final adaptor-ligated fragments. Quality and quantity were assessed on High Sensitivity dsDNA Agilent Bioanalyzer Chips and Quibit. WT and OGA-null O-GlcNAc-seq libraries and OGA ChIP-seq libraries were sequenced on the Illumina NextSeq 500 High Output (75 cycles, 400M reads) platform. The additional replicates for both WT and OGA-null DMSO control from an earlier pilot study were sequenced on the MiSeq platform, using v3, 150-cycle reagent kits (Illumina).

treatment_protocol: Wild-type OGA knockout (OGA-null) Drosophila (P. T. Radermacher, F. Myachina, F. Bosshardt, R. Pandey, D. Mariappa, H.-A. J. Müller, C. F. Lehner, Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 5592–5597) were expanded in 50 mL bottles of cornmeal molasses media at 25°C. Drosophila parents from approximately 25 of these bottles were required for each time course replicate. Time course Ac4GalNAz feeding was performed on 10 mL petri dishes. Just under 10 mL of cornmeal molasses media supplemented with Ac4GalNAz dissolved in DMSO to a final concentration of 150 uM or DMSO only in the same volume added to the Ac4GalNAz plates (control) were made. Adult Drosophila parents from the bottles were then transferred to the control plates for 2 hours (on cages) for a pre-egg laying period. This facilitated the laying of eggs that were not synchronized. These adult Drosophila were then transferred to either 150 uM Ac4GalNAz or control plates for 2 hours (enabling the laying of synchronized eggs). After a 36 h incubation period, the resulting larvae were transferred to control plates or collected and snap frozen (0 h time point). Larvae that were initially grown on control plates were collected at this time as well (no feed control). The larvae transferred from Ac4GalNAz plates to control plates were then collected after 4, 8, 12, 16, 20, 24, and 36 hours of feeding on these control plates.

tag: genotype/variation

value: GalNAz feeding, strain-promoted click reaction and streptavidin purification


title: blASCs.WGBS.r3

description: bisulfite treated  genomic DNA

tag: cell subtype

value: blASCs


title: EED_chiapet_rep2

description:
allPRC2_chiapet.narrowPeak.gz
allPRC2.cis.chiasig.sigf.interactions.gz

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) v0.0.1a (https://github.com/cheehongsg/CPU). CPU (options: tag -W) removed the adaptors, and extracted the intra-molecular and inter-molecular paired tags based on the linker sequence identified in the read and the remaining read-pairs without linker sequence. Tags (>=18bp) and reads without linker sequence were mapped to mouse genome (mm10) independently  using CPU (options: memaln -T 15), which utilized BWA (options: aln and mem) according to the tag/read length. CPU (options: pair) further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration. Next, deduplication of uniquely-mapped pair-end tags/reads arising from clonal PCR amplification was performed with CPU (options: dedup).
The non-redundant uniquely-mapped pair-end tags are merged with samtools and deduplicated with CPU (options: dedup) for all replicates of each factor separately, producing 3 factor-level (i.e. Suz12, Ezh2, Eed) alignment files. PRC2 binding peaks were called with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B –SPMR -g mm) where the 3 factor-level alignment files are specified as the treatment file and the combined 28 input files (23 E14_input, 2 CTCF ChIP input, 2 H3K27me3 ChIP input and RNAPolII_ChIP_r1_input) as the input control.
The non-redundant uniquely-mapped pair-end tags are merged with samtools and deduplicated with CPU (options: dedup) for all replicates of each factor separately, producing 3 factor-level (i.e. Suz12, Ezh2, Eed) alignment files. These 3 factor-level alignment files were merged using samtools and clustering of the pair-end tags were performed with CPU (options: cluster -M -B 1000 -v 3 -5 5,-20 -3 5,980 -g) to produce cis-interactions and trans-interactions. Statistical assessment of the cis-interaction significance was performed using ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -p -m 3000). Cis-interaction clusters with member size 3 and above (iPET 3+) and FDR<0.05 were reported, excluding any interaction should any of its anchors overlap the blacklist (see publication supplementary table).
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

tag: cell line

tag: ip antibody

value: EED (Abcam ab4469)


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 24h growth on DMSO media

description:
ogako.r2_24
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 24h growth on DMSO media

source_name: O-GlcNAc-seq_OGA KO larvae_150uM GalNAz media for 36h followed by 24h growth on DMSO media


title: CTCF_ChIP_rep1_input


title: OGA ChIP-seq in WT Drosophila larvae

description:
wt-OGA-ChIP-seq
processed data file: OGA-ChIP-seq-peaks.bed
OGA ChIP-seq in WT Drosophila larvae

source_name: OGA ChIP-seq_WT larvae

value: wild type


title: Nup107.rep2

value: Embryonic cells

value: Nup107 (this study)


title: E14_RNA-seq_rep1

value: E14 cell line

value: embryonic stem cells


title: blASCs.WGBS.r2

description: bisulfite treated  genomic DNA


title: RNApolII_chiapet_rep3


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 20h growth on DMSO media

description:
ogako.r2_20
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 20h growth on DMSO media

source_name: O-GlcNAc-seq_OGA KO larvae_150uM GalNAz media for 36h followed by 20h growth on DMSO media


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 12h growth on DMSO media

description:
ogako.r2_12
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 12h growth on DMSO media

source_name: O-GlcNAc-seq_OGA KO larvae_150uM GalNAz media for 36h followed by 12h growth on DMSO media


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 16h growth on DMSO media

description:
ogako.r2_16
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 16h growth on DMSO media

source_name: O-GlcNAc-seq_OGA KO larvae_150uM GalNAz media for 36h followed by 16h growth on DMSO media


title: EZH2_chiapet_rep3

value: Ezh2 (Active Motif 39875)


title: blASCs.WGBS.r1

description: bisulfite treated  genomic DNA

value: Embryonic stem cell


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 8h growth on DMSO media

description:
ogako.r2_8
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 8h growth on DMSO media

source_name: O-GlcNAc-seq_OGA KO larvae_150uM GalNAz media for 36h followed by 8h growth on DMSO media


title: S2-L7-rep3

value: lamin L7 antibody


title: EZH2_chiapet_rep2


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 4h growth on DMSO media

description:
ogako.r2_4
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 4h growth on DMSO media

source_name: O-GlcNAc-seq_OGA KO larvae_150uM GalNAz media for 36h followed by 4h growth on DMSO media


title: SUZ12_chiapet_rep9

value: Suz12 (Abcam ab12073)


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 24h growth on DMSO media

description:
ogako.r1_24
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 24h growth on DMSO media


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_DMSO media for 36h

description:
ogako.r1_no-feed
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on DMSO media for 36h

source_name: O-GlcNAc-seq_OGA KO larvae_DMSO media for 36h


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 36h growth on DMSO media

description:
ogako.r1_36
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 36h growth on DMSO media


title: BCL.ESCs.r1

description: polyA RNA

source_name: Embryonic stem cell


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 2)_150uM GalNAz media for 36h followed by 0h growth on DMSO media

description:
ogako.r2_0
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 2) grown on 150uM GalNAz media for 36h followed by 0h growth on DMSO media

source_name: O-GlcNAc-seq_OGA KO larvae_150uM GalNAz media for 36h followed by 0h growth on DMSO media


title: BCL.ESCs.r2

description: polyA RNA


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 20h growth on DMSO media

description:
ogako.r1_20
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 20h growth on DMSO media


title: BCL.ESCs.r3

description: polyA RNA


title: ACL.ESCs.r3

description: polyA RNA


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 16h growth on DMSO media

description:
ogako.r1_16
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 16h growth on DMSO media


title: SUZ12_chiapet_rep8


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 12h growth on DMSO media

description:
ogako.r1_12
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 12h growth on DMSO media


title: SUZ12_chiapet_rep7


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 8h growth on DMSO media

description:
ogako.r1_8
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 8h growth on DMSO media


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 4h growth on DMSO media

description:
ogako.r1_4
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 4h growth on DMSO media


title: ACL.ESCs.r2

description: polyA RNA


title: O-GlcNAcseq_OGA KO Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 0h growth on DMSO media

description:
ogako.r1_0
processed data file: TC-O-GlcNAc-seq-peaks.bed
O-GlcNAc-seq in OGA knockout Drosophila larvae (biological replicate 1) grown on 150uM GalNAz media for 36h followed by 0h growth on DMSO media