title: SNAIL_Induction_Day6_Replicate_1

city: Charlestown

first: Robert

last: Morris

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

data_processing:
Reads aligned using STAR v2.4.0h aligner with default settings
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed
The uniquely aligned reads were counted using htseq-count in the intersection-strict mode.
Genome_build: GRCh38.79
Supplementary_files_format_and_content: Tab delimited text file containing the raw read counts for each annotated feature.

source_name: MCF10A cell line, SNAIL_Induction_Day6

growth_protocol: MCF10A cells grown in classical media with treatment with 5ng/ml of TGFB for 1 and 6 days. MC10A-Snail, expressing the inducible ER:SNAILS6A- stablilized version of SNAIL: inducible by tamoxifen, for 1 or 6 days. Cells are passages every 3 days.

extract_protocol:
RNA was extracted by RNA easy kit from Quiagen.
RNA was processed using the TruSeq Stranded Total RNA-seq library construction kit (Illumina) per protocol, which uses a ribosomal depletion followed by RNA fragmentation and random hexameter based complementary DNA synthesis.  Libraries were barcoded and sequenced on the NextSeq 500 platform using the 300 cycle High output kit (FC-404-1004) for 150 pair end sequencing.

treatment_protocol: TGFB at 5ng/ml or 4OH-Tamoxifen at 10-7M


title: SNAIL_Induction_Day1_Replicate_1

status: Public on Jan 30 2017

type: SRA

state: Massachusetts

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: MCF10A cell line, SNAIL_Induction_Day1

tag: cell line


title: SNAIL_Induction_Day0_Replicate_1

source_name: MCF10A cell line, SNAIL_Induction_Day0


title: TGFB_Induction_Day1_Replicate_2

source_name: MCF10A cell line, TGFB_Induction_Day1


title: 15hpa

city: Stanford

first: Jessica

middle: Kay

last: Chang

state: CA

address: 300 Pasteur Drive, Alway Building M311

department: Genetics

institute: Stanford University

data_processing:
Adapter sequences and low quality bases were trimmed using fastx_clipper (fastx_toolkit v 0.13.2) for single end reads and trim_galore v 0.3.3 for paired end libraries.  Reads were subsequently mapped to the v9.0 genome via Tophat v2.0.13 with very-sensitive parameters.
Multimapped or unmapped reads were filtered using samtools v 1.1.
Count data was summarized via HTSeq (python v2.7).  Adjustments for sequencing depth (and prior to clustering, variance stabilization through rlog transformation) were performed using DESeq2 (R v3.2.0).
Genome_build: Xentr9.0
Supplementary_files_format_and_content: Tab delimited file containing normalized count data (adjusted by size factor via DESeq2).  Additional columns concerning whether a gene was called differentially expressed (DE) or if it was assigned to a fuzzy cluster are also included.

organism: Xenopus tropicalis

source_name: Tadpole tail

extract_protocol:
Tadpole tails were amputated and immediately placed in lysis buffer (1% SDS, 0.100M NaCl, 0.010M EDTA, 0.20M Tris ph 7.6, Proteinase K) followed by ethanol precipitation to extract RNA. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Tadpole

tag: age

value: Stage 40

tag: treatment

value: Tadpole tails were amputated

tag: time

value: 15hours post-amputation

tag: tissue

value: Tail


title: TGFB_Induction_Day6_Replicate_2

source_name: MCF10A cell line, TGFB_Induction_Day6


title: 0hpa_rep2

value: 0hours post-amputation


title: TGFB_Induction_Day0_Replicate_2

source_name: MCF10A cell line, TGFB_Induction_Day0


title: 0hpa_rep1


title: 6hpa

value: 6hours post-amputation


title: WT_rep2

value: control


title: TGFB_Induction_Day1_Replicate_1


title: WT_rep1


title: TGFB_Induction_Day6_Replicate_1


title: DE_Input rep1

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

library_source: genomic

data_processing:
Mapping : bowtie -m 2 --maxIns 350
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
Processing: Plot of density of alignments in a moving 300 bp window with an increment of 30  bp
Genome_build: mm9
Supplementary_files_format_and_content: bigWig : un-normalised coverage of filtered fragments (reconstructed, duplicate-filtered fragments : see above),  density of alignments in a moving 300 bp window with an increment of 30  bp

molecule: genomic DNA

organism: Mus musculus

source_name: Definitive Endoderm

growth_protocol: Definitive Endoderm differentiation from ESCs cultured as EBs for 2 days, induced to differentiate to a DE fate in N2B27 medium supplemented with ActivinA and EGF. EBs were dissociated by incubation with 0.25% trypsin (Gibco) for 3 min at 37˚C with constant agitation followed by gentle pipetting to obtain a single cell suspension.

extract_protocol:
Fixed cells were lyzed on ice for 20 minutes (5 mM PIPES, 85 mM KCl, 0.5% Igepal-CA 630) before pelleting and nuclear lysis (50 mM Tris-HCl, 10 mM EDTA, 1% SDS), chromatin was then sonicated to 200bp in a Covaris S220 and incubated overnight with 2 µl of anti-H3K4me3 (07-473; Millipore) and Protein A and Protein G Dynabeads (Invitrogen). Beads were washed seven times with RIPA buffer variants (10 mM Tris-HCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate): RIPA (twice), High Salt RIPA (500 mM NaCl; twice), RIPA with 250mM LiCl (once) and T.E. Buffer (twice) before treatment with RNAse A at 37ºC for 1 hr (Roche) and Proteinase K 65ºC overnight (Thermo Fisher). DNA was recovered by phenol-chloroform extraction.
Libraries were indexed for sequencing using NebNext Ultra II (New England BioLabs); library profiles were visualized using D1000 tape on a TapeStation (Agilent Technologies) and quantified using a universal library quantification kit (KAPA Biosystems).

treatment_protocol: ES cells (ESC) were seeded in suspension at low density (1x104 cells/ml) in the absence of LIF to form embryoid bodies (EBs). ES cells were seeded in DMEM (Invitrogen) supplemented with 15% fetal calf serum (Gibco), 1% Penicillin/Streptomycin (Invitrogen), 0.1mM 2-mercaptoethanol (Sigma), 1% Glutamine (Invitrogen), 1% MEM Non-essential amino acids (Gibco) and 1mM Sodium Pyruvate (Sigma). On day 2 EBs were transferred into N2B27 medium (Cellartis) supplemented with 20ng/ml ActivinA (R&D systems) and 20ng/ml EGF (Peprotech) to induce DE differentiation (Morrison et al. 2008).

tag: cell type

value: ES_derived Definitive Endoderm

tag: strain

tag: day of differentiation

value: Day 5

tag: chip antibody


title: ObBPA_3

status: Public on Jan 29 2017

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
QC: We checked the quality of the raw reads data for each sample using FastQC [1] (version 0.10.1) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).
Aligment: We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, we aligned reads to the reference transcriptome (Ovis Aries Oar_v3.1.81_genes.gtf) using TopHat (version 2.0.9) and Bowtie (version 2.1.0.). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: We used Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis, using Ovis Aries Oar_v3.1.81_genome.fa as the reference genome sequence. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Differential Expression: We used locally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ ± 1.5.
Annotation: When possible, we annotated genes and isoforms with NCBI Entrez GeneIDs and text descriptions. We further annotated differentially expressed genes with Gene Ontology (GO) terms using NCBI annotation.
Genome_build: Ovis Aries Oar_v3.1.81
Supplementary_files_format_and_content: text table of normalized expression values for each gene for each sample

molecule: polyA RNA

organism: Ovis aries

extract_protocol:
Harvesting of heart tissue was conducted during the second breeding season, when the selected animals were 21 months old. All animals were given two 20 mg injections of Prostaglandin F2α (PGF2α, 5 mg/mL Lutalyse; Pfizer Animal Health, NY, USA), 11 days apart, to induce luteolysis and synchronize the initiation of the follicular phase in cycling females. Ewes were euthanized after the second PGF2α injection, during the presumptive follicular phase, by administration of a barbiturate overdose (Fatal Plus, Vortech Pharmaceuticals, Dearborn, MI).  Hearts were dissected out and weighed, then myocardium was harvested from a randomly selected subset of four animals per group (n=4 for each of the control, BPA, obese, and ObBPA groups) and quick frozen until processed. Total RNA was extracted from the frozen myocardium using TRIzol Reagent (Life Technologies) according to the manufacturer’s instructions. The concentration of RNA from each sample was measured by NanoDrop 2000 UV-Vis Spectrophotometer (Thermo Scientific). OD 260/280 values were 1.87 - 1.96 for the RNA samples. The integrity of each RNA sample was monitored through Agilent BioA RNA Integrity Number (RIN).
RNA-Seq was performed by the Genomic Sequencing Core (GSC) in the University of Cincinnati. Using the TruSeq RNA sample preparation kit (Illumina), one µg of total RNA with RIN (Agilent 2100 Bioanalyzer) ³ 7.0 was used to purify poly-A containing mRNA using poly-T oligo-attached magnetic beads. The purified mRNA was enzymatically fragmented and random hexamers-primed for the first and second strand cDNA synthesis, followed by purification using Agencourt AMPure XP beads (Beckman Coulter).The double-strand cDNA with overhangs was converted into blunt ends in the end repair procedure, and adenylated to add a single "A" nucleotide at 3' ends to prevent them from self-ligation in the following ligation step. The AMPure XP beads-purified fragments were then ligated to sample-specific indexing adapters, and enriched by 10 cycles' of PCR using adapter-specific primers.One µl of purified PCR product (sequencing library, total 30 µl) was analyzed by Bioanalyzer (Agilent) using the DNA 1000 chip to check the DNA fragment size (~260 bp) and yield. To accurately quantify the library concentration for the clustering, the library was 1:104-106 diluted in dilution buffer (10 mM Tris-HCl, pH 8.0 with 0.05% Tween 20), and qPCR analyzed by the Kapa Library Quantification kit (Kapabiosystem) using ABI's 9700HT real-time PCR system

treatment_protocol: Pregnant ewes in  BPA treatment group spanned days 30 through 90 of gestation and consisted of daily sc injections of 0.5 mg/kg/day of BPA (purity ≥ 99%, cat# 239658; Aldrich Chemical Co., Milwaukee, WI), with corn oil as the vehicle. Pregnant ewes in the control group were administered vehicle alone. They female offspring beginning at 14 weeks of age were separated by diet.  The daily diet of the control-fed animals, on a per lamb basis, consisted of 1.4 lbs corn, 0.03 lbs of supplement (36% crude protein), and 1.4 lbs hay. The daily diet of overfed animals consisted of 1.7 lbs corn, 0.03 lbs of supplement, and 1.6 lbs hay initially and then ad libitum. To compensate for increased energy demands as the lambs grew, and to meet additional energy demands during inclement weather, the ration was increased in control-fed and overfed females by the same percentages. To avoid confounding effects from differences in feeds, all feed was purchased in bulk. Beginning six weeks before the expected date of delivery and continuing until the time of delivery, pregnant ewes were group-fed 0.5 kg shelled corn, 2 kg alfalfa hay and 250 mg aureomycin crumbles (chlortetracycline)/ewe/day. Lactating ewes were fed 1 kg shelled corn and 2-2.5 kg of alfalfa hay/ewe/day. All lambs and ewes were provided with water and minerals ad libitum and were treated regularly with antihelminthics to minimize parasitic infection. From weaning to 14 weeks of age, all lambs had ad libitum access to commercial feed pellets (Shur-Gain, Elma, NY, USA; contains 18% crude protein) and alfalfa hay.

value: ObBPA

value: myocardium

tag: gender

value: female


title: ObBPA_2


title: ObBPA_1


title: DE_H3K4me3 rep1

value: anti-H3K4me3 (07-473; Millipore)


title: 24hpa_rep1

value: 24hours post-amputation


title: obese_3

value: obese


title: obese_2


title: obese_0


title: obese_1


title: BPA_3

value: BPA


title: TGFB_Induction_Day0_Replicate_1


title: BPA_2


title: control_2


title: 786O, 0 mM glucose medium

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: LucG

data_processing:
The LifeScope v2.5.1 was used to align the reads to the genome, generate raw counts corresponding to each gene, and calculate the RPKM (reads per kilobase per million) values.
Genome_build: Hg19
Supplementary_files_format_and_content: text file with RPKM values.

source_name: 786O, 0 mM glucose medium

growth_protocol: 786-O cells were cultured with or without glucose

extract_protocol:
RNA was harvested using Trizol reagent
Library construction protocol not provided.

value: human kidney cancer cells


title: BPA_1


title: 786O, 25 mM glucose medium

description: LucF

source_name: 786O, 25 mM glucose medium

extract_protocol:
RNA was harvested using Trizol reagent.
Library construction protocol not provided.


title: Fcre/cre

city: Shanghai

first: Bin

last: Li

address: 320 Yueyang Road, Xuhui District,

country: China

institute: Institut Pasteur of Shanghai, CAS

data_processing:
Basecalling by Illumina Casava1.7 software
Raw reads were filtered with fastx (version:0.0.13) and then mapped to mm10 whole genome using tophat (version:2.0.9)
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using cufflinks (version:2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: excel files include FPKM and count values for both  WT and UKO Treg cells

source_name: Spleen&LN

extract_protocol:
Spleen and LN were removed and separated into single cells.Treg cells were solted by FACS.RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: WT; Foxp3-YFP-Cre

value: 6-month old

value: spleen and lymph node

value: CD4+CD25hiYFP+ Treg cells


title: UKO

value: UKO; Foxp3-YFP-Cre/USP21-floxp/floxp


title: control_1


title: control_3


title: BPA_0


title: E2F1_rep2_ChIPSeq

city: San Antonio

first: Zhenqing

last: Ye

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

description: ChIP DNA

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Casava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with default parameters
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig file

source_name: Prostate cells

growth_protocol: PC3 cells were routinely generated by regular cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in RPMI1640 medium (Gibco, USA) supplemented with 10% serum (Gibco, USA).

extract_protocol:
Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: passages

tag: antibodies

value: E2F1 (Santa Cruz, C-20, lot SC-193)


title: E2F1_rep1_ChIPSeq

description: ChIP DNA


title: LSD1_rep1_ChIPSeq

description: ChIP DNA

value: LSD1 (Abcam, lot ab17721)


title: input DNA

description: input DNA


title: ObBPA_0


title: C

status: Public on Jan 28 2017

first: Gai

middle: Ni

last: Ma

address: ziyue road

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science Shanghai, CHINA

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to Sscrofa10.2  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Sus scrofa

source_name: no IFN treatment, uninfected (Control)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

value: pulmonary alveolar macrophages


title: V

source_name: no IFN treatment, infected with PRRSV


title: IFNV

source_name: treated with IFN, infected with PRRSV


title: IFN

source_name: treated with IFN, uninfected


title: U2OS-dTFdox_RNAseq

city: Tempe

first: Karmella

last: Haynes

state: Arizona

address: 501 E Tyler Mall, Box 9709

department: SBHSE

institute: Arizona State University

description:
Sample 9
Control used to compute relative abundance of transcripts in U2OS-PcTFdox_RNAseq1, U2OS-PcTFdox_RNAseq2, U2OSpos_RNAseq.
Processed data file: U2OS-PcTF_rel_abundance_1x3.txt
Processed data file: U2OS-PcTF_DESeq_2x3.pdf

data_processing:
Two to four raw read files were produced per sample and concatenated prior to processing.
Raw sequence data (fastq) was analyzed with FastQC.
TrimmomaticSE was used to remove low-quality reads and adapters.
Within the public Galaxy online platform, splice junctions were mapped using Tophat (Galaxy version 2.1.0) and Bowtie 2 (default parameters) to generate BAM files.
Cuffdiff relative abundance for single trial RNA-seq (1x1): Within the Galaxy online platform the BAM output files, "accepted_hits (bam)," and the Illumina igenomes hg19 gtf file were used as input for Cuffdiff with the following parameters: Library normalization method = classic-fpkm, Dispersion estimation method = blind, False Discovery Rate = 0.05, Min Alignment Count = 10, Use multi-read correct = True, Perform Bias Correction / Include Read Group Datasets / Include Count Based output files = No, apply length correction = cufflinks effective length correction, Average Fragment Length = 200, Fragment Length Standard Deviation = 80, Set Advanced Cuffdiff parameters? / Job Resource Parameters = No.
Cuffdiff relative abundance for replicate trial RNA-seq (1x3): Same as 1x1 except Dispersion estimation method = pooled.
In the "gene differential expression testing" output files, rows containing the following 28 outdated gene annotations were removed using the Galaxy "Filter and Sort: Filter" and "Join, Subtract and Group: Subtract Whole Dataset" commands: AGSK1, AKIRIN2-AS1, DDX11L9, C10orf58, FAM75A2, FAM75A7, C9orf174, FAM90A10, FAM90A7, FLJ10661, LOC100170939, LOC100286793, LOC100505815, LOC100509575, LOC143188, LOC145663, LOC150527, LOC401431, LOC440297, LOC646508, LOC727710, MIR1280, PRINS, PRO0611, RP1-177G6.2, RP11-165H20.1, TRIM78P, XAGE2B.
DESeq differential expression for replicate trail RNA-seq (2x3): In Galaxy, the ht-seq count tool was used for each BAM file and the Illumina igenomes hg19 gtf file with the following parameters: Mode = Union, Stranded = Yes, Minimum alignment quality = 10, Feature type = exon, ID Attribute = gene_id, Additional BAM Output = False, Force sorting of SAM/BAM file by NAME = False. Ht-seq count output files were used as input for the DESeq2 tool with the following parameters: Visualising the analysis results = True, Fit type = parametric, others set to "false."
Genome_build: Human Feb. 2009 (GRCh37/hg19)
Supplementary_files_format_and_content: Relative abundance: tab-delimited txt files with the following columns: test_id, gene_id, gene, locus, sample_1 (untreated), sample_2 (treated), status, value_1 (untreated FPKM), value_2 (treated FPKM), log2(fold_change) test_stat, p_value, q_value, significant. Differential expression (DEseq): pdf file.

source_name: U2OS-dTF transgenic, dox treated

growth_protocol: Cells were grown up to ~5.0E5 cells in 6-well plates at 37 deg. C in a 5% CO2 humidified incubator in the following media supplemented with 10% Tet-free FBS and 1% penicillin/ streptomycin: U-2 OS in McCoy's 5A, SK-N-SH in EMEM, K562 in IMDM. Pen/strep was omitted during transient transfections (to reduce toxicity) and replaced after 18 hours.

extract_protocol:
Total messenger RNA was extracted from ~90% confluent cells (~1-2x10^6). Adherent cells (U2OS and SK-N-SH) were lysed directly in culture plates with 500 μl TRIzol. Suspended cells (K562) were collected into tubes, pelleted by centrifugation at 1000 xg for 3 min. at room temperature, separated from the supernatant, and lysed in 500 μl TRIzol. TRIzol cell lysates were extracted with 100 μl chloroform and centrifuged at 12,000 xg for 15 min. at 4°C. RNA was column-purified from the aqueous phase (Qiagen RNeasy Mini kit 74104).
50 ng of total RNA was used to prepare cDNA via single primer isothermal amplification using the Ovation RNA-Seq System (Nugen 7102-A01) and automated on the Apollo 324 liquid handler (Wafergen). cDNA was sheared to approximately 300 bp fragments using the Covaris M220 ultrasonicator. Libraries were generated using Kapa Biosystem’s library preparation kit (KK8201). In separate reactions, fragments from each replicate sample were end-repaired, A-tailed, and ligated to index and adapter fragments (Bioo, 520999). The adapter-ligated molecules were cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883), and amplified with Kapa’s HIFI enzyme. The library was analyzed on an Agilent Bioanalyzer, and quantified by qPCR (KAPA Library Quantification Kit, KK4835) before multiplex pooling and sequencing on a HiSeq 2000 platform (Illumina) at the ASU CLAS Genomics Core facility.

treatment_protocol: Samples 1, 3, and 5 (transfections): DNA/Lipofectamine complexes contained 2 μg of plasmid DNA, 7.5 μl of Lipofectamine LTX (Invitrogen), 2.5 PLUS reagent, and 570 µl OptiMEM. Transfected cells were grown in pen/strep-free growth medium for 18 hrs. The transfection medium was replaced with fresh, pen/strep-supplemented medium and cells were grown for up to 48 hrs. (K562) or up to 96 hrs (U-2 OS and SK-N-SH). Controls (samples 2, 4, 6) were treated with vehicle only (Lipofectamine, PLUS, OptiMEM). Samples 7-10 (transgenic) were treated with 1 ug/mL doxycycline for 96 hours.

value: U2OS-dTF KAH132

tag: protein

value: delta-TF (truncated)

tag: tag

value: untreated (deactivated protein)


title: U2OSdTFpos_RNAseq

description:
Sample 10
Processed data file: U2OS-PcTF_DESeq_2x3.pdf

source_name: U-2 OS transfected with dTF plasmid

tag: cell line

value: U-2 OS (ATCC HTB-96)


title: U2OS-PcTFdox_RNAseq2

description:
Sample 8
Processed data file: U2OS-PcTF_rel_abundance_1x3.txt
Processed data file: U2OS-PcTF_DESeq_2x3.pdf

source_name: U2OS-PcTF transgenic, dox-treated

value: U2OS-PcTF KAH126

value: PcTF

value: treated


title: U2OS-PcTFdox_RNAseq1

description:
Sample 7
Processed data file: U2OS-PcTF_rel_abundance_1x3.txt
Processed data file: U2OS-PcTF_DESeq_2x3.pdf


title: K562neg_RNAseq

description:
Sample 6
Control used to compute relative abundance of transcripts in K562pos_RNAseq.
Processed data file: K562pos_rel_abundance_1x1.txt

value: untreated


title: control_0

value: control

value: myocardium

value: female


title: K562pos_RNAseq

description:
Sample 5
Processed data file: K562pos_rel_abundance_1x1.txt

source_name: K562 transfected with PcTF plasmid


title: LSD1_rep2_ChIPSeq

description: ChIP DNA


title: U2OSpos_RNAseq

description:
Sample 1
Processed data file: U2OSpos_rel_abundance_1x1.txt
Processed data file: U2OS-PcTF_rel_abundance_1x3.txt
Processed data file: U2OS-PcTF_DESeq_2x3.pdf

source_name: U-2 OS transfected with PcTF plasmid


title: U2OSneg_RNAseq

description:
Sample 2
Control used to compute relative abundance of transcripts in U2OSpos_RNAseq.
Processed data file: U2OSpos_rel_abundance_1x1.txt

source_name: U-2 OS


title: SKNSHneg_RNAseq

description:
Sample 4
Control used to compute relative abundance of transcripts in SKNSHpos_RNAseq.
Processed data file: SKNSHpos_rel_abundance_1x1.txt

source_name: SK-N-SH

value: SK-N-SH (ATCC HTB-11)


title: SKNSHpos_RNAseq

description:
Sample 3
Processed data file: SKNSHpos_rel_abundance_1x1.txt

source_name: SK-N-SH transfected with PcTF plasmid


title: PC9M + GNF5

city: Durha

first: Jing Jin

last: Gu

state: NC

address: 308 Research Dr.

department: Pharmacology and Cancer Biology

institute: Duke University

description: supplementary file: PC9M Control-GNF5.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using tophat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff based on the protocol Cole Trapnell et al. Nature Biotechnology 31, 46-53 (2013)
Genome_build: hg18
Supplementary_files_format_and_content: diff files include RPKM values for each Sample

source_name: non-small cell lung carcinoma

growth_protocol: All cells were cultured in RPMI1640medium + 10% FBS + 10mM HEPES, 1 mM Sodium Pyruvate and 0.2% glucose.

extract_protocol:
RNA was harvested using Qiagen Rneasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treaned with or without GNF5 (10mM for PC9 and H358, 20 mM for PC9M) ofr 72 hrs or  transduced with either scrambled or ABL1/ABL2-specific shRNAS in the presence of 8ug/mL Polybrene.

tag: subtype

value: adenocarcinoma

tag: metastasis

value: more bone-brain metastasis

tag: knockdown


title: PC9M Control

value: DMSO


title: H358 Control

description: supplementary file: H358 Control-GNF5.xlsx

value: not tested


title: PC9 ABL1/ABL2 shRNAs

description: supplementary file: PC9 SCR-AA.xlsx

value: general Metastasis

value: ABL1/ABL2-specific shRNAs


title: PC9M ABL1/ABL2 shRNAs

description: supplementary file: PC9M SCR-AA.xlsx


title: PC9 + GNF5

description: supplementary file: PC9 Control-GNF5.xlsx


title: PC9M Scrambled shRNA

description: supplementary file: PC9M SCR-AA.xlsx

value: scrambled shRNA


title: Alzheimer’s-affected human brain

city: Rourkela

first: Dr. Bibekanand

last: Mallick

state: Odisha

address: NIT Rourkela

department: Department of Life Science

country: India

institute: National Institute of Technology

description: small RNA

data_processing:
bcl2fastq software (Illumina) was used for converting image file to FASTq format.
Sequenced reads were trimmed for adaptor sequence using srna Work bench, and Quality check of the generated data was done using the FASTqc software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of annotated piRNAs identified in each Sample. A text file contains the read counts for miRNAs.

source_name: Total RNA from Alzheimer’s-affected brain

extract_protocol:
Total RNA isolated using modified guanidine thiocyanate technique from healthy human and Alzheimer’s disease brain was procured from BioChain, USA. The purity of isolated RNA was examined using NanoDrop spectrophotometer (Thermo Scientific) by measuring absorbance at 260 nm and 280 nm. An aliquot of each the samples was also run on an Agilent RNA Bioanalyzer to check the RNA integrity number (RIN) and was found to be 8.1 and 8.5 in HB and AD sample respectively.
The RNA libraries were constructed for sequencing following Illumina TruSeq Small RNA library protocol outlined in “TruSeq Small RNA Sample Preparation Guide” (Part # 15004197; Rev. F; February 2014) and using TruSeq Small RNA sample preparation kit (Illumina, # RS-200-0012).

value: brain

tag: diagnosis

value: Alzheimer's disease


title: Healthy human brain

description: small RNA

source_name: Total RNA from human brain

tag: tissue

value: normal brain


title: 7d.3

city: Miami

first: Jae

middle: K.

last: Lee

state: FL

address: 1095 NW 14th Terrace

institute: University of Miami Miller School of Medicine

data_processing:
reads were aligned to the mouse reference genome (mm10) using Tophat version 2.0.12 with a combined reference genome annotation (UCSC, Ensembl, and RefSeq)
reads assembled into transcripts using Cufflinks version 2.2
gene expression levels estimated and normalized using Cuffquant version 2.2.1
differential expression tested using Cuffdiff version 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include offical gene name, locus, FPKM for each sample, mean FPKM for each group, log2 fold change, test statistic, p-value, q-value, and whether the differential expression is significant
Supplementary_files_format_and_content: All genes, differential expression
Supplementary_files_format_and_content: Filtered genes, differential expression

source_name: Spinal cord

extract_protocol:
RiboTag immunoprecipitation from spinal cord injury site of LysMCre:Rplfl/fl > CD45.1 chimeras followed by RNA isolation
ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina)

treatment_protocol: T8 contusive SCI

tag: genotype

value: LysMCre:Rplfl/fl > CD45.1 chimera

value: Spinal cord injury site


title: PC9 Control


title: H358 + GNF5


title: 7d.2

tag: strain


title: 7d.1


title: 3d.3


title: AML_R1+FLT3_EtOH_rep1

city: Hamburg

first: Kira

last: Behrens

address: Martinistrasse 52

country: Germany

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

description: GFP+BFP+CD11b-Gr1-_AML cultured 22h w EtOH

data_processing:
base calling was performed using RTA 1.18.64.0
RNA-seq reads were aligned to the mm9 genome assembly using CLC Genomics Workbench v6.5.1 software (Qiagen) using default settings
No data filtering steps were used
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

growth_protocol: For AML_R1+FLT3_EtOH_rep1, AML_R1+FLT3_EtOH_rep2, AML_R1+FLT3_4-OHT_rep1, AML_R1+FLT3_4OHT_rep2 bone marrow was extracted form leukemic mice and cultured for 22h in SFEM + FLT3L + SCF + IL3 +IL11. Remaining samples were sorted and sequenced immediately after isolation from sick mice.

extract_protocol:
RNA was extracted from FACS-sorted cells using the peqGOLD TriFast kit (Peqlab) according to the manufacturer's instructions
Libraries were generated using the TruSeq: RNA Sample Preparation V2 Low Throughput (LT) Kit (Illumina) or the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (both from New England Biolabs)

treatment_protocol: For AML_R1+FLT3_EtOH_rep1, AML_R1+FLT3_EtOH_rep2, AML_R1+FLT3_4-OHT_rep1, AML_R1+FLT3_4OHT_rep2 bone marrow cells were treated either with 200nM 4OHT or equivalent volume of EtOH.

tag: cell type


title: AML_R1+FLT3_EtOH_rep2


title: ALL_FLT3_rep1


title: AML_R1+FLT3_4OHT_rep2

description: GFP+BFP+CD11b-Gr1-_AML cultured 22h w 4OHT


title: 3d.2


title: ALL_FLT3_rep2


title: 3d.1


title: AML_R1+FLT3_rep1

description: whole BM


title: AML_R1+FLT3_rep2

description: whole BM


title: PC9 Scrambled shRNA

description: supplementary file: PC9 SCR-AA.xlsx


title: AML_A/E_rep2

description: GFP+venus+kit+ AML

value: A/E+ AML


title: BS_seq_MALE_MEF_3

status: Public on Jan 27 2017

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description:
BS-seq (PBAT)
BS_seq_MALE_MEF_3.cov.gz

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters) and mapped to the mouse NCBIM37 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Trimmed sequences were mapped to the mouse NCBIM37 genome using Bismark (Krueger and Andrews, 2011) (v0.12.3, parameters --bowtie2); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts. Global methylation comparison was calculated by averaging 1kb window methylation levels of CpGs covered by at least 30 reads.
Genome_build: NCBIM37
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: Quantitated RNA-Seq data files are tab delimited and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7) RPKM value

source_name: BS seq MALE MEF 3

extract_protocol:
DNA samples were bisulfite converted using EZ-DNA Methylation-Direct reagent (Zymo Research). Strand-specific libraries were made using the PBAT protocol described in (Milagre et al. 2017). Briefly, a random elongation reaction was performed with primers containing truncated versions of the illumina sequencing primers, and a PCR amplification was performed using KAPA Uracil+ ReadyMix (KAPA Biosystems) and illumina primer sequences. Pooling was conducted using sanger iTags.
Genomic DNA and RNA were isolated from the same samples using the Allprep DNA/RNA kit (Qiagen).

tag: background strain

tag: time-point in reprogramming

value: MEF

value: Wild-type Male


title: AML_A/E_rep1

description: GFP+kit+ AML


title: AML_R1+FLT3_4OHT_rep1


title: Combinatorial scHi-C Library ML3

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

data_processing:
Library strategy: Hi-C-seq
Reads were mapped to a combined Burrows-Wheeler reference of hg19 and mm10 using bowtie2. They were then filtered using custom Python scripts to generate validPairs files (see README file on series record).

organism:
Homo sapiens
Mus musculus

source_name: Cultured Cell Lines

growth_protocol: Cells are grown under standard tissue culture conditions (10 - 15% FBS, 5% CO2, DMEM or RPMI media, and 1X Pen-Strep) as the Coriell culture practices demand)

extract_protocol:
Cells are lysed using 0.2% NP-40; 10 mM NaCl; 10 mM Tris pH 8.0 in ddH2O
Combinatorial single-cell Hi-C is carried out using a similar protocol to the insitu Hi-C and in situ DNase protocols

treatment_protocol: Cells are fixed using 2% (HeLa, HAP1, GM12878, K562, MEF) or 2.5% (Patski) formaldehyde.

tag: cell lines

value: Contains K562, GM12878, Patski, and primary MEF cells


title: BS_seq_MALE_MEF_2

description:
BS-seq (PBAT)
BS_seq_MALE_MEF_2.cov.gz

source_name: BS seq MALE MEF 2


title: BS_seq_d60_MALE_iPSC_Clone1

description:
BS-seq (PBAT)
BS_seq_d60_MALE_iPSC_Clone1.cov.gz

source_name: BS seq d60 MALE iPSC Clone1

value: late passage iPSC


title: BS_seq_d60_MALE_iPSC_Clone2

description:
BS-seq (PBAT)
BS_seq_d60_MALE_iPSC_Clone2.cov.gz

source_name: BS seq d60 MALE iPSC Clone2


title: BS_seq_MALE_MEF_1

description:
BS-seq (PBAT)
BS_seq_MALE_MEF_1.cov.gz

source_name: BS seq MALE MEF 1


title: BS_seq_d60_MALE_iPSC_Clone3

description:
BS-seq (PBAT)
BS_seq_d60_MALE_iPSC_Clone3.cov.gz

source_name: BS seq d60 MALE iPSC Clone3


title: BS_seq_d29_MALE_iPSC_Clone1

description:
BS-seq (PBAT)
BS_seq_d29_MALE_iPSC_Clone1.cov.gz

source_name: BS seq d29 MALE iPSC Clone1

value: early passage iPSC


title: BS_seq_d21_iPSC_Clone3

source_name: BS seq d21 iPSC Clone3

extract_protocol:
DNA samples were fragmented by sonication (Covaris) and adaptor ligated using Illumina supplied methylated adaptors and NEBnext library preparation kit. DNA was bisulfite treated using the TrueMethyl kit (Cambridge Epigenetix).
Genomic DNA and RNA were isolated from the same samples using the Allprep DNA/RNA kit (Qiagen).

value: Wild-type


title: BS_seq_d29_MALE_iPSC_Clone3

description:
BS-seq (PBAT)
BS_seq_d29_MALE_iPSC_Clone3.cov.gz

source_name: BS seq d29 MALE iPSC Clone3


title: BS_seq_d29_MALE_iPSC_Clone2

description:
BS-seq (PBAT)
BS_seq_d29_MALE_iPSC_Clone2.cov.gz

source_name: BS seq d29 MALE iPSC Clone2


title: BS_seq_d29_iPSC_Clone2

source_name: BS seq d29 iPSC Clone2


title: BS_seq_d60_iPSC_Clone2

source_name: BS seq d60 iPSC Clone2


title: BS_seq_d60_AIDKO_iPSC_Clone2

source_name: BS seq d60 AIDKO iPSC Clone2

value: AIDKO


title: BS_seq_d29_iPSC_Clone3

source_name: BS seq d29 iPSC Clone3


title: BS_seq_AIDKO_MEF2

source_name: BS seq AIDKO MEF2


title: BS_seq_d60_AIDKO_iPSC_Clone1

source_name: BS seq d60 AIDKO iPSC Clone1


title: RNA_seq_d60_iPSC_Clone3

source_name: RNA seq d60 iPSC Clone3

extract_protocol:
RNA was DNase treated with the DNA-free kit (Life Technologies). mRNA was purified from 50 ng of total RNA, using a Dynabeads® mRNA Purification Kit (Life Technologies).  Strand-specific libraries were generated as previously described (Wang et al., 2011).
Genomic DNA and RNA were isolated from the same samples using the Allprep DNA/RNA kit (Qiagen).


title: BS_seq_AIDKO_MEF1

source_name: BS seq AIDKO MEF1


title: RNA_seq_d29_iPSC_Clone3

source_name: RNA seq d29 iPSC Clone3


title: RNA_seq_d21_iPSC_Clone2

source_name: RNA seq d21 iPSC Clone2


title: RNA_seq_d60_iPSC_Clone2

source_name: RNA seq d60 iPSC Clone2


title: RNA_seq_d29_iPSC_Clone2

source_name: RNA seq d29 iPSC Clone2


title: RNA_seq_d21_iPSC_Clone3

source_name: RNA seq d21 iPSC Clone3


title: RNA_seq_d60_AIDKO_iPSC_Clone1

source_name: RNA seq d60 AIDKO iPSC Clone1


title: RNA_seq_d60_AIDKO_iPSC_Clone2

source_name: RNA seq d60 AIDKO iPSC Clone2


title: BS_seq_d29_AIDKO_iPSC_Clone2

source_name: BS seq d29 AIDKO iPSC Clone2


title: RNA_seq_d29_AIDKO_iPSC_Clone2

source_name: RNA seq d29 AIDKO iPSC Clone2


title: RNA_seq_d29_AIDKO_iPSC_Clone1

source_name: RNA seq d29 AIDKO iPSC Clone1


title: BS_seq_d60_iPSC_Clone3

source_name: BS seq d60 iPSC Clone3


title: BS_seq_d21_iPSC_Clone2

source_name: BS seq d21 iPSC Clone2


title: RNA_seq_AIDKO_MEF1

source_name: RNA seq AIDKO MEF1


title: #3-D6F

city: La Jolla

first: Tianxu

last: Han

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference sequences using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Supplementary_files_format_and_content: xlsx files include normalized reads of each shRNA

source_name: ES-derived cells

extract_protocol:
The genomic DNA of sorted cells were routinely extracted.
The sequences corresponding to each shRNA were PCR amplified using universal primers, digested with XhoI and EcoRI restriction enzymes, and gel purified. The purified fragments were then used for preparation of a sequencing library according to the Illumina Hi-seq kit instructions.

value: ES-derived mesodermal/endothelium cells

tag: sorting strategy


title: #3-D20LS

value: ES-derived non-hematopoietic and differentiated cells


title: #3-D20LK

value: ES-derived hematopoietic cells


title: #3-D6C

value: ES-derived endodermal cells


title: #3-D20LKS

value: ES-derived hematopoietic progenitor cells


title: #2-D20LKS


title: RNA_seq_AIDKO_MEF2

source_name: RNA seq AIDKO MEF2


title: #2-D6F


title: BS_seq_d29_AIDKO_iPSC_Clone1

source_name: BS seq d29 AIDKO iPSC Clone1


title: #2-ESC

source_name: ESC

value: ESC


title: #2-D20LK


title: #1-D20LKS


title: #3-ESC


title: #1-D20LS


title: #2-D20LS


title: #1-D20LK


title: #1-D6C


title: #1-ESC


title: #1-D6F


title: RNA_Seq_d60 iPSC_Clone1

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters) and mapped to the mouse NCBIM37 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Trimmed sequences were mapped to the mouse NCBIM37 genome using Bismark (Krueger and Andrews, 2011) (v0.12.3, parameters --bowtie2); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts. Global methylation comparison was calculated by averaging 1kb window methylation levels of CpGs covered by at least 30 reads.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Bismark coverage report: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: Quantitated RNA-Seq data files are tab delimited and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7) RPKM value

source_name: RNA Seq P29 iPSC Clone1


title: RNA_Seq_d6_SSEA1_positive_3

source_name: RNA Seq d6 SSEA1 positive 3


title: RNA_Seq_d21 iPSC_Clone1

source_name: RNA Seq P8 iPSC Clone1


title: RNA_Seq_d6_SSEA1_positive_2

source_name: RNA Seq d6 SSEA1 positive 2


title: RNA_Seq_d6_SSEA1_positive_1

source_name: RNA Seq d6 SSEA1 positive 1


title: RNA_Seq_d6_Thy1_positive_3

source_name: RNA Seq d6 Thy1 positive 3

value: d6 Thy1+/SSEA1-


title: RNA_Seq_d6_Thy1_positive_2

source_name: RNA Seq d6 Thy1 positive 2


title: RNA_Seq_d6_Thy1_positive_1

source_name: RNA Seq d6 Thy1 positive 1


title: RNA_Seq_ESC_3

source_name: RNA Seq ESC 3

value: d6 Thy1-/SSEA1+


title: RNA_Seq_ESC_2

source_name: RNA Seq ESC 2


title: RNA_Seq_ESC_1

source_name: RNA Seq ESC 1


title: #2-D6C


title: RNA_Seq_MEF_3

source_name: RNA Seq MEF 3


title: RNA_Seq_MEF_1

source_name: RNA Seq MEF 1


title: BS_seq_d6_SSEA1_positive_3

source_name: BS seq d6 SSEA1 positive 3


title: BS_seq_d21 iPSC_Clone1

source_name: BS seq P8 iPSC Clone1


title: BS_seq_d29 iPSC_Clone1

source_name: BS seq P12 iPSC Clone1


title: BS_seq_d6_SSEA1_positive_2

source_name: BS seq d6 SSEA1 positive 2


title: BS_seq_d6_Thy1_positive_3

source_name: BS seq d6 Thy1 positive 3


title: BS_seq_d6_Thy1_positive_1

source_name: BS seq d6 Thy1 positive 1


title: BS_seq_ESC_3

source_name: BS seq ESC 3


title: BS_seq_d6_SSEA1_positive_1

source_name: BS seq d6 SSEA1 positive 1


title: BS_seq_ESC_1

source_name: BS seq ESC 1


title: BS_seq_ESC_2

source_name: BS seq ESC 2


title: BS_seq_d6_Thy1_positive_2

source_name: BS seq d6 Thy1 positive 2


title: BS_seq_MEF_2

source_name: BS seq MEF 2


title: BS_seq_MEF_3

source_name: BS seq MEF 3


title: BS_seq_MEF_1

source_name: BS seq MEF 1


title: BS_seq_d60 iPSC_Clone1

source_name: BS seq P29 iPSC Clone1


title: Perivascular endfeet translatome [Endfeet2]

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-alpha5. Before mapping, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from Ensembl version 75) using the Bowtie mapper (version 0.12.9, parameters -n 2 -l 34 -e 70 -k 2 –best). Alignments from reads matching more than once on the genome were removed. Mus musculus GFF3 genome annotation from from Ensembl version mm10-ens75 was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: mm10 version Ensembl 75
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

source_name: Perivascular endfeet translatome

extract_protocol:
BAC array purification;  mRNAs were purified following the bacTRAP immnuoprecipitation protocol using GFP antibodies and further purified using the RNAeasy protocol (Qiagen).
Ovation RNA-Seq system NuGEN

value: Aldh1L1 JD130

tag: genotype/variation

tag: age

value: 2 months

value: Purified brain vessels

tag: molecule subtype

value: polysome mRNAs


title: Perivascular endfeet translatome [Endfeet5]


title: Perivascular endfeet translatome [Endfeet4]


title: Perivascular endfeet translatome [Endfeet6]


title: Perivascular endfeet translatome [Endfeet1]


title: BrdU-negative_BrdU-IP-Seq_S-phase_rep2

city: Beijing

first: Qing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Science

institute: Peking University

data_processing:
After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed
BrdU enriched regions were called by the dpos function in DANPOS 2.2.2.
Reads coverage were calculated by the dregion function in DANPOS 2.2.2. And the read coverage were normalized by background noise.
Nucleosome score were calculated by the dpos function in DANPOS 2.2.2.
An exponential function of 3 independent parameters was used to simulate DNA replication pattern. Simulation was performed by least-square method in fit toolbox of MATLAB (2014b, MathWork).
The ReIN-Map Score representing replication-coupled nucleosome assembly level was calculated by results of BrdU-IP-Seq and MNase-BrdU-IP-Seq.
Genome_build: sacCer3
Supplementary_files_format_and_content: default wiggle (WIG) format

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown on YPD at 30°C and were arrested at G1 phase with alpha-factor, and then released into fresh YPD media containing 0.2 M Hydroxyurea and 400μg/ml BrdU for 45min.

extract_protocol:
Cells released into YPD without BrdU were lysed by beads-beating and following sonication to fragment the chromatin to an average size around 100-400bp. The DNA were purified with ethanol precipitation. The purified DNA were further heat denatured for BrdU IP and ssDNA library preparation.
DNA prepared above were immobilized on MyOne C1 beads (Life Technology). Primers were added by PCR and adaptors by ligation. Then DNA were eluted as ssDNA at 95°C. The ssDNA were amplified by PCR reaction, and the amount of each sample was verified by qPCR. Verified sample DNA were sequenced by Illumina HiSeq generating 100bp pair-ended reads.

treatment_protocol: Cells were crosslinked with PFA at 25°C 180rpm for 20min, and PFA was quenched by Glycine.

value: wild type

tag: cell cycle stage

value: Early S phase


title: Whole astrocyte translatome [Astrocyte3]

source_name: Whole astrocyte translatome

value: Brain


title: Whole astrocyte translatome [Astrocyte2]


title: BrdU-negative_MNase-BrdU-IP-Seq_S-phase_rep2

extract_protocol:
Cells released into YPD without BrdU were spheroplasted with zymolase digestion and following treatment with micrococcal nuclease (MNase) to digest into mononucleosomes. The DNA were purified with ethanol precipitation. The purified DNA were further heat denatured for BrdU IP and ssDNA library preparation.
DNA prepared above were immobilized on MyOne C1 beads (Life Technology). Primers were added by PCR and adaptors by ligation. Then DNA were eluted as ssDNA at 95°C. The ssDNA were amplified by PCR reaction, and the amount of each sample was verified by qPCR. Verified sample DNA were sequenced by Illumina HiSeq generating 100bp pair-ended reads.


title: Whole astrocyte translatome [Astrocyte1]


title: RNA_Seq_MEF_2

source_name: RNA Seq MEF 2

value: MEF

value: Wild-type


title: BrdU-negative_MNase-BrdU-IP-Seq_S-phase_rep1


title: rtt109d_DNA-Seq_S-phase_rep2

extract_protocol:
Cells were lysed by beads-beating and following sonication to fragment the chromatin to an average size around 100-400bp. The DNA were purified with ethanol precipitation. The purified DNA were further heat denatured for ssDNA library preparation.
DNA prepared above were immobilized on MyOne C1 beads (Life Technology). Primers were added by PCR and adaptors by ligation. Then DNA were eluted as ssDNA at 95°C. The ssDNA were amplified by PCR reaction, and the amount of each sample was verified by qPCR. Verified sample DNA were sequenced by Illumina HiSeq generating 100bp pair-ended reads.


title: rtt109d_BrdU-IP-Seq_S-phase_rep1

extract_protocol:
Cells were lysed by beads-beating and following sonication to fragment the chromatin to an average size around 100-400bp. The DNA were purified with ethanol precipitation. The purified DNA were further heat denatured for BrdU IP and ssDNA library preparation.
DNA prepared above were immobilized on MyOne C1 beads (Life Technology). Primers were added by PCR and adaptors by ligation. Then DNA were eluted as ssDNA at 95°C. The ssDNA were amplified by PCR reaction, and the amount of each sample was verified by qPCR. Verified sample DNA were sequenced by Illumina HiSeq generating 100bp pair-ended reads.


title: rtt109d_MNase-BrdU-IP-Seq_S-phase_rep1

extract_protocol:
Cells were spheroplasted with zymolase digestion and following treatment with micrococcal nuclease (MNase) to digest into mononucleosomes. The DNA were purified with ethanol precipitation. The purified DNA were further heat denatured for BrdU IP and ssDNA library preparation.
DNA prepared above were immobilized on MyOne C1 beads (Life Technology). Primers were added by PCR and adaptors by ligation. Then DNA were eluted as ssDNA at 95°C. The ssDNA were amplified by PCR reaction, and the amount of each sample was verified by qPCR. Verified sample DNA were sequenced by Illumina HiSeq generating 100bp pair-ended reads.


title: rtt109d_MNase-BrdU-IP-Seq_S-phase_rep2


title: rtt109d_BrdU-IP-Seq_S-phase_rep2


title: rtt109d_MNase-Seq_S-phase_rep2

extract_protocol:
Cells were spheroplasted with zymolase digestion and following treatment with micrococcal nuclease (MNase) to digest into mononucleosomes. The DNA were purified with ethanol precipitation. The purified DNA were further heat denatured for ssDNA library preparation.
DNA prepared above were immobilized on MyOne C1 beads (Life Technology). Primers were added by PCR and adaptors by ligation. Then DNA were eluted as ssDNA at 95°C. The ssDNA were amplified by PCR reaction, and the amount of each sample was verified by qPCR. Verified sample DNA were sequenced by Illumina HiSeq generating 100bp pair-ended reads.


title: rtt109d_MNase-Seq_S-phase_rep1


title: rtt109d_DNA-Seq_G1-phase_rep1

value: G1 phase


title: rtt109d_MNase-Seq_G1-phase_rep1


title: A88P_BrdU-IP-Seq_S-phase_rep1


title: A88P_MNase-BrdU-IP-Seq_S-phase_rep2


title: A88P_BrdU-IP-Seq_S-phase_rep2


title: Perivascular endfeet translatome [Endfeet3]


title: A88P_MNase-BrdU-IP-Seq_S-phase_rep1


title: BrdU-negative_BrdU-IP-Seq_S-phase_rep1


title: A88P_DNA-Seq_S-phase_rep2


title: A88P_DNA-Seq_S-phase_rep1


title: A88P_MNase-Seq_S-phase_rep2


title: A88P_DNA-Seq_G1-phase_rep1


title: A88P_MNase-Seq_G1-phase_rep1


title: A88P_MNase-Seq_G1-phase_rep2


title: A88P_DNA-Seq_G1-phase_rep2


title: WT_BrdU-IP-Seq_S-phase_rep1


title: WT_MNase-BrdU-IP-Seq_S-phase_rep1


title: WT_MNase-BrdU-IP-Seq_S-phase_rep2


title: WT_BrdU-IP-Seq_S-phase_rep2


title: WT_DNA-Seq_G1-phase_rep2


title: rtt109d_DNA-Seq_G1-phase_rep2


title: WT_MNase-Seq_S-phase_rep1


title: WT_DNA-Seq_G1-phase_rep1


title: rtt109d_MNase-Seq_G1-phase_rep2


title: rtt109d_DNA-Seq_S-phase_rep1


title: Mid_Oxygen_CC Rep_1

city: Richland

first: Ryan

middle: Scott

last: McClure

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

data_processing:
The 50-base short read sequences produced by the 5500XL SOLiD  sequencer were mapped in color space using SOLiD LifeScope software version 2.5 using the default parameters
Raw counts for each file were then normalized using DESeq2, this program was also used to identify differentially expression genes (defined as >2.0 fold change with an adjusted p-value of < 0.05).
Genome_build: Thermosynechococcus elongatus BP1: NC_004113
Supplementary_files_format_and_content: T_Elongatus_Norm_Counts.csv

organism: Thermosynechococcus vestitus BP-1

source_name: Planktonic cells

growth_protocol: Growth took place in a bioreactor at pH 7.5, 52C, in modified BG-11 media (BP1 media, mM): 17.6 NaNO3, 0.3039 MgSO4∙7H2O, 0.175 KH2PO4, 0.2449 CaCl2∙2H2O, 0.0028 Na2EDTA, 0.0144 FeCl3. The mBG-11 was supplemented with 1 ml L-1 trace-mix (mM): 46.2544 H3BO3, 9.1458 MnCl2∙4H2O, 0.7720 ZnSO4∙7H2O, 1.6119 Na2MoO4∙2H2O, 0.3164 CuSO4∙5H2O, 0.1697 Co(NO3)2∙6H2O.

extract_protocol:
RNA was extracted using Trizol following by DNAseI treatment using Qiagen RNAseay mini column
Template cDNA was prepared using the Applied Biosystems SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) according to manufacturer's protocol. Sequencing was carried using the SOLiDTM 5500XL protocol (Life Technologies).

treatment_protocol: Three light levels were examined: low (197 µmol photons m-2 sec-1), mid (1190 µmol photons m-2 sec-1), and high (1995 µmol photons m-2 sec-1) all with oxygen at at a partial pressure of 0 .  Three oxygen levels were also examined: low (partial pressure of oxygen=0), mid (partial pressure of oxygen=0.3) and high (partial pressure of oxygen=0.6) all at a light level of 197 µmol photons m-2 sec-1.  T. elongatus was examined both axenically and with a hetertrophic partner of each of these six conditions.  The high light condition overlaps with the low oxygen condition for both axenic and co-culture experiments

tag: oxygen

value: Mid

tag: light

value: High

tag: axenic vs. coculture

value: Coculture


title: Mid_Oxygen_CC Rep_2


title: High_Oxygen_CC Rep_1


title: WT_MNase-Seq_G1-phase_rep2


title: High_Oxygen_CC Rep_2


title: WT_MNase-Seq_G1-phase_rep1


title: WT_DNA-Seq_S-phase_rep2


title: A88P_MNase-Seq_S-phase_rep1


title: High_Oxygen_AX Rep_2

value: Axenic


title: WT_DNA-Seq_S-phase_rep1


title: WT_MNase-Seq_S-phase_rep2


title: High_Light_CC Rep_1

value: Low


title: Mid_Oxygen_AX Rep_1


title: High_Oxygen_AX Rep_1


title: Low_Light_CC Rep_1


title: Mid_Light_AX Rep_2


title: High_Light_AX Rep_2


title: Low_Light_AX Rep_2


title: MgSO4_stress_low: MURI_171

city: AUSTIN

first: Mehmet

middle: Umut

last: Caglar

state: Texas

address: 2500 Speedway, A4800

department: Integrative Biology

institute: UNIVERSITY OF TEXAS AUSTIN

data_processing:
trim adaptors on raw reads and moved trimmed reads to trimmed_reads with flexbar
bowtie2-build final_reference_seqs/REL606.fa indexes/REL606
map trimmed reads to reference sequence in indexes file with bowtie2
convert bowtie output .sam to .bam with samtools
convert back to sorted.sam with samtools
get raw counts for reads mapped with htseq-count
Genome_build: reference sequence is REL606
Supplementary_files_format_and_content: txt files including count numbers of RNA's and quality control were generated

organism: Escherichia coli B str. REL606

source_name: stationary culture

extract_protocol:
RNAsnap followed by purification through Zymo RNA clean and concentrator.
Illumina Ribozero rRNA removal followed by NEB Next RNA library Prep set.

tag: growth time (hours)

tag: growth phase

value: stationary

tag: carbon source

value: glucose

tag: mg+2 (mm)

tag: mg+2 (levels)

value: lowMg

tag: na+1 (mm)

tag: na+1 (levels)

value: baseNa

tag: batch


title: Mid_Oxygen_AX Rep_2


title: Mid_Light_CC Rep_1


title: Mid_Light_CC Rep_2


title: Low_Light_AX Rep_1


title: Mid_Light_AX Rep_1


title: Low_Light_CC Rep_2


title: High_Light_CC Rep_2


title: MgSO4_stress_low: MURI_170


title: High_Light_AX Rep_1


title: MgSO4_stress_low: MURI_168


title: MgSO4_stress_low: MURI_169


title: Foxl1 positive rep3

city: Philadelphia

first: Michal

last: Shoshkes-Carmel

state: PA

address: 3400 Civic Center Blvd, 12-161

institute: University of Pennsylvania

description:
10820
FGC1446_s_7_CGTACTAGTATCCTCT

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: mm9
Supplementary_files_format_and_content: Excel format file of transcript raw read counts of each sample
Supplementary_files_format_and_content: Excel format file of FPKM read counts of each sample

source_name: intestine mesenchyme

extract_protocol:
Intestine mesenchyme was dissociated to single cells by 7mg/ml DispaseII/0.05% trypsin solution 15 minutes 37℃. Cells were sorted lysed and total RNA was isolated by column purification (Absolutely RNA Nanoprep kit; Agilent Technologies)
NEB Next RNA library prep kit (New England BioLabs, Inc)

tag: strain

value: mixed

tag: tissue

value: intestine mesenchyme

tag: genotype

value: Foxl1Cre; Rosa-mTmG


title: MgSO4_stress_low: MURI_167


title: MgSO4_stress_low: MURI_166

source_name: exponential culture

value: exponential


title: Foxl1 positive rep2

description:
8953
FGC1342_s_6_TGACCA

value: Foxl1Cre; Rosa-YFP


title: IRF1ko_24hrs_Th0_2

city: Cincinnati

first: Emily

middle: R

last: Miraldi

state: Ohio

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: accessible DNA

data_processing:
Sequences were mapped to the murine genome (mm9) with bowtie2
Sequences were filtered (MAPQ>30) with Samtools
Duplicates were removed using Picard
Peakdeck (parameters -bin 75, -STEP 25, -back 10000, -npBack 100000) was used to call peaks (Praw < 1E-4)
A reference set of peaks was found by taking peak maxima for each sample, extending +/-25bp and merging peaks from each sample
HTSeq-count was used to map reads to reference peaks
DESeq2 was used to quantify peak accessibility across samples and test for differential accessibility
Genome_build: mm9
Supplementary_files_format_and_content: DESeq2-normalized (RLOG) quantification for all ATAC-seq peaks and differential analysis (fold-changes, p-values, etc.) for select comparisons, peak annotations (nearest TSS, transcription factor motifs found within the peak, etc.)

source_name: Naïve CD4+ T cells, activated with anti-CD3/CD28 for 24 hrs

growth_protocol: CD4+ T cells were purified from spleen and lymph node using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-CD4-PerCP, anti-CD62L-APC, and anti-CD44-PE antibodies (all Biolegend, CA). Naïve CD4+ CD62Lhigh CD44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-CD3 (2μg/ml) and anti-CD28 (2μg/ml) for a specific number of hours.

extract_protocol:
Cells harvest was followed by a transposition reaction and purification (Buenrostro  et al. Curr Protoc Mol Biol. 2015)
Prepared as in Buenrostro  et al. Curr Protoc Mol Biol. 2015

treatment_protocol: 25ng/ml rmIL-27, cells were cultured for 24h or 72h

value: spleen and lymph node

tag: cell type

tag: time point

value: IRF1 KO


title: MgSO4_stress_low: MURI_164


title: BATFko_24hrs_Th0_1

description: accessible DNA

value: BATF KO


title: MgSO4_stress_low: MURI_165


title: MgSO4_stress_low: MURI_163


title: MgSO4_stress_low: MURI_162


title: BATFko_72hrs_Th0_2

description: accessible DNA


title: Foxl1 positive rep1

description:
8372
FGC1184_s_5_TGACCA


title: MgSO4_stress_low: MURI_161


title: BATFko_72hrs_Th0_1

description: accessible DNA


title: IRF1ko_24hrs_Th0_1

description: accessible DNA


title: MgSO4_stress_low: MURI_158


title: MgSO4_stress_low: MURI_157


title: MgSO4_stress_low: MURI_153


title: MgSO4_stress_low: MURI_154


title: MgSO4_stress_low: MURI_159


title: MgSO4_stress_low: MURI_160


title: Tr1_BATFko_24h_2

description: accessible DNA

source_name: Naïve CD4+ T cells, activated with anti-CD3/CD28 for 24 hrs in the presence of IL27


title: Tr1_24h_1

description: accessible DNA

value: CONTROL


title: IRF1ko_72hrs_Th0_1

description: accessible DNA


title: IRF1ko_72hrs_Th0_2

description: accessible DNA


title: Tr1_BATFko_24h_1

description: accessible DNA


title: MgSO4_stress_low: MURI_152


title: Th0_24h_2

description: accessible DNA


title: MgSO4_stress_low: MURI_156


title: MgSO4_stress_low: MURI_151


title: Tr1_BATFko_72h_2

description: accessible DNA

source_name: Naïve CD4+ T cells, activated with anti-CD3/CD28 for 72 hrs in the presence of IL27


title: Th0_24h_1

description: accessible DNA


title: MgSO4_stress_low: MURI_150


title: BATFko_24hrs_Th0_2

description: accessible DNA


title: Tr1_BATFko_72h_1

description: accessible DNA


title: Tr1_IRFko_72h_2

description: accessible DNA


title: MgSO4_stress_low: MURI_148


title: MgSO4_stress_low: MURI_147


title: Tr1_IRFko_72h_1

description: accessible DNA


title: MgSO4_stress_low: MURI_146


title: Tr1_IRFko_24h_1

description: accessible DNA


title: Tr1_24h_2

description: accessible DNA


title: Tr1_IRFko_24h_2

description: accessible DNA


title: MgSO4_stress_low: MURI_155


title: Tr1_72h_2

description: accessible DNA


title: MgSO4_stress_low: MURI_145


title: Tr1_72h_1

description: accessible DNA


title: MgSO4_stress_low: MURI_144


title: MgSO4_stress_low: MURI_143


title: MgSO4_stress_high: MURI_141

value: highMg


title: Tr1_AHRko_1

description: accessible DNA

value: AHR KO


title: MgSO4_stress_low: MURI_142


title: Tr1_AHRko_2

description: accessible DNA


title: Tr1_cMaf_flfl_2

description: accessible DNA


title: MgSO4_stress_high: MURI_140


title: MgSO4_stress_high: MURI_137

value: baseMg


title: Tr1_BATFko_1

description: accessible DNA


title: Tr1_cMafCre_2

description: accessible DNA

value: MAF KO


title: MgSO4_stress_high: MURI_138

value: stationary


title: Tr1_cMaf_flfl_1

description: accessible DNA


title: MgSO4_stress_high: MURI_134

value: glucose


title: MgSO4_stress_high: MURI_136

value: lowMg


title: MgSO4_stress_high: MURI_135

value: baseNa


title: Tr1_IRF1ko_2

description: accessible DNA


title: MgSO4_stress_high: MURI_133


title: Tr1_IRF1ko_1

description: accessible DNA


title: MgSO4_stress_high: MURI_132


title: MgSO4_stress_low: MURI_149


title: Th0_72h_2

description: accessible DNA

source_name: Naïve CD4+ T cells, activated with anti-CD3/CD28 for 72 hrs


title: Tr1_2

description: accessible DNA


title: Th0_72h_1

description: accessible DNA


title: MgSO4_stress_high: MURI_131


title: Tr1_cMafCre_1

description: accessible DNA


title: MgSO4_stress_high: MURI_139


title: Th0_2

description: accessible DNA


title: Tr1_1

description: accessible DNA


title: MgSO4_stress_high: MURI_130


title: MgSO4_stress_high: MURI_129


title: MgSO4_stress_high: MURI_127


title: MgSO4_stress_high: MURI_128


title: Tr1_72h_39

data_processing:
sequences were mapped to the murine geneome (mm10) using STAR
HTSeq-count was used to map sequences to genes
DESeq2 was used to normalize and identify differentially transcripts across conditions
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2-normalized (RLOG) quantification for genes across all samples and differential analysis (fold-changes, p-values, etc.) for select comparisons
Supplementary_files_format_and_content: Tr1_RNAseq_VSDcounts.txt: DESeq2-normalized (VSD) quantification for genes across all samples
Supplementary_files_format_and_content: Tr1_RNAseq_diffTable.txt: DESeq2 differential analysis (fold-changes, p-values, etc.) for select comparisons
Supplementary_files_format_and_content: Tr1_RNAseq_mcolVsd.txt: DESeq2 per-gene factor estimates for the model: gene expression ~ genotype + Batch

growth_protocol: CD4+ T cells were purified from spleen and lymph node using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-CD4-PerCP, anti-CD62L-APC, and anti-CD44-PE antibodies (all Biolegend, CA). Naïve CD4+ CD62Lhigh CD44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-CD3 (2μg/ml) and anti-CD28 (2μg/ml) in the presence of IL27.

extract_protocol:
Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
Libraries were prepared for sequencing using RNAtag-Seq (Shishkin et al, Nat Methods 2015)

treatment_protocol: 25ng/ml rmIL-27, cells were cultured for 72 hours

value: WT


title: Tr1_BATFko_2

description: accessible DNA


title: MgSO4_stress_high: MURI_125


title: MgSO4_stress_high: MURI_124


title: Tr1_Irf1Ko_72h_36

value: Irf1 KO


title: Tr1_Irf1Ko_72h_43


title: MgSO4_stress_high: MURI_123


title: MgSO4_stress_high: MURI_122


title: Tr1_BatfKo_72h_38

value: Batf KO


title: Tr1_72h_41


title: MgSO4_stress_high: MURI_120

value: exponential


title: MgSO4_stress_high: MURI_118


title: Tr1_BatfKo_72h_39


title: MgSO4_stress_high: MURI_116


title: MgSO4_stress_high: MURI_119


title: MgSO4_stress_high: MURI_126


title: MgSO4_stress_high: MURI_117


title: Th0_1

description: accessible DNA


title: MgSO4_stress_high: MURI_115


title: MgSO4_stress_high: MURI_114


title: MgSO4_stress_high: MURI_111


title: MgSO4_stress_high: MURI_113


title: MgSO4_stress_high: MURI_121


title: HsInt-Input

city: Singapore

first: Aditi

last: Qamra

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: GIS

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) ‘aln’ algorithm for histone ChIP-seq. Sequence reads were mapped against  hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.7) ‘aln’ algorithm for EZH2 ChIP-seq
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads to perform peak calling using CCAT v3.0 [local FDR < 0.05] for histone ChIP-seq and MACS2 [local FDR <0.1]
Genome_build: hg19
Supplementary_files_format_and_content: interval format for ucsc genome browser, including 8 columns: "chromosome" "position of the peak" "start of region" "end of region" "read counts in ChIP library" "read counts in control library" "fold-change score" "local FDR". narrowPeaks format for ucsc genome browser, including 10 columns: "chromosome" "start of region" "end of region" "peakid","integer score for display","strand","fold-change","-log10pvalue","-log10qvalue","relative summit position to peak start"

source_name: Gastric Cancer Line

extract_protocol: Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). ChIPs were performed using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam); H3K36me3 (ab9050, Abcam); H3K27me3 (07-449, Millipore),EZH2 (# 5246, Cell Signaling) using same chromatin preparation.

treatment_protocol: Fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized pieces for each ChIP. Tissue pieces were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer. For cell lines, 1 million fresh harvested cells were fixed in 1% formaldehyde/medium buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Fixed cells were washed 3 times with TBSE buffer, and centrifuged (5,000 r.p.m., 5 min).

tag: tissue type

value: Hs 1.Int

tag: chip antibody

value: Input


title: Tr1_72h_35

value: spleen and lymph node


title: MgSO4_stress_high: MURI_108


title: MgSO4_stress_high: MURI_110


title: Hs738-Input

value: Hs 738.St/Int


title: HsInt-G-K4me3


title: MgSO4_stress_high: MURI_107


title: Hs738-K4me3


title: HFE145-Input


title: glucose_time_course: MURI_104

source_name: late stationary culture


title: MgSO4_stress_high: MURI_112


title: glucose_time_course: MURI_105


title: glucose_time_course: MURI_102


title: MgSO4_stress_high: MURI_106


title: glucose_time_course: MURI_101


title: glucose_time_course: MURI_100


title: glucose_time_course: MURI_097


title: glucose_time_course: MURI_098


title: gluconate_growth: MURI_091

value: gluconate


title: gluconate_growth: MURI_096


title: glucose_time_course: MURI_099


title: gluconate_growth: MURI_095


title: gluconate_growth: MURI_094


title: gluconate_growth: MURI_093


title: lactate_growth: MURI_088

value: lactate


title: HsInt-K4me3


title: NaCl_stress: MURI_084

value: highNa


title: gluconate_growth: MURI_092

value: baseMg


title: lactate_growth: MURI_090


title: Tr1_Irf1Ko_72h_42


title: lactate_growth: MURI_089


title: MgSO4_stress_high: MURI_109

value: highMg


title: glucose_time_course: MURI_103

value: stationary


title: lactate_growth: MURI_086


title: lactate_growth: MURI_085


title: NaCl_stress: MURI_077

value: glucose


title: NaCl_stress: MURI_083


title: NaCl_stress: MURI_079


title: NaCl_stress: MURI_070


title: NaCl_stress: MURI_068


title: NaCl_stress: MURI_076


title: NaCl_stress: MURI_080


title: NaCl_stress: MURI_065


title: NaCl_stress: MURI_082


title: NaCl_stress: MURI_069


title: NaCl_stress: MURI_074


title: NaCl_stress: MURI_075


title: lactate_growth: MURI_087


title: NaCl_stress: MURI_064


title: glycerol_time_course: MURI_059

value: glycerol


title: NaCl_stress: MURI_061

value: baseNa


title: glycerol_time_course: MURI_056


title: NaCl_stress: MURI_073


title: glycerol_time_course: MURI_058


title: NaCl_stress: MURI_071


title: NaCl_stress: MURI_072


title: NaCl_stress: MURI_067


title: NaCl_stress: MURI_081


title: NaCl_stress: MURI_066


title: glycerol_time_course: MURI_052


title: NaCl_stress: MURI_063


title: glycerol_time_course: MURI_057


title: glycerol_time_course: MURI_049


title: glycerol_time_course: MURI_045


title: glycerol_time_course: MURI_055


title: glycerol_time_course: MURI_040


title: glycerol_time_course: MURI_053


title: glycerol_time_course: MURI_054


title: glycerol_time_course: MURI_050


title: glycerol_time_course: MURI_038


title: glycerol_time_course: MURI_036


title: glycerol_time_course: MURI_048


title: glycerol_time_course: MURI_041


title: glycerol_time_course: MURI_047


title: glycerol_time_course: MURI_046


title: glycerol_time_course: MURI_044


title: glucose_time_course: MURI_032


title: glucose_time_course: MURI_030


title: glycerol_time_course: MURI_035


title: glucose_time_course: MURI_028


title: glycerol_time_course: MURI_042


title: glucose_time_course: MURI_026


title: glycerol_time_course: MURI_043


title: glycerol_time_course: MURI_037


title: glycerol_time_course: MURI_039


title: glycerol_time_course: MURI_034


title: glucose_time_course: MURI_033


title: glucose_time_course: MURI_023


title: glucose_time_course: MURI_024


title: glucose_time_course: MURI_021


title: glucose_time_course: MURI_031


title: glucose_time_course: MURI_020


title: glucose_time_course: MURI_019


title: glucose_time_course: MURI_017


title: glucose_time_course: MURI_029


title: glucose_time_course: MURI_018


title: LAC_rpiRC

status: Public on Jan 26 2017

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values for each gene were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Samples were compared using "Set Up Experiment" tool for transcriptomic analysis using CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The S. aureus USA300 FPR3757 genome file was accessed from GenBank (Accesion number:CP000255)
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: AH LAC rpiRC::bursa

value: AH LAC carrying the bursa aurealis transposon in the rpiRC gene

tag: growth medium

value: TSB

tag: growth conditions (time/temp/shaking)


title: glucose_time_course: MURI_022

tag: growth time (hours)


title: LAC_wt

value: AH LAC

value: wild-type


title: HFE145-K4me3


title: glucose_time_course: MURI_027

tag: growth phase

value: exponential


title: glucose_time_course: MURI_016

tag: carbon source


title: glucose_time_course: MURI_025

tag: mg+2 (mm)


title: RRBS_GM0227

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: UCLA

data_processing:
RRBS library reads were mapped to the hg19 reference genome using BS-Seeker v2.0.32 (Guo et al., 2013), which called bowtie v0.12.9  (Langmead et al., 2009). Reads with adapter contamination were trimmed. The adapter sequence used for the contamination check was as follows: CGAGATCGGAAGAGCACACGTC, i.e. meCG end repair + A tail + 10.bp of Illumina adapter sequence.
Genome_build: hg19
Supplementary_files_format_and_content: CGmap files are produced by BS-Seeker2 and contain C and T counts per cytosine for both strands.
Supplementary_files_format_and_content: The format is fully described here: https://github.com/BSSeeker/BSseeker2#output-files
Supplementary_files_format_and_content: Briefly, each column of the represents the following:
Supplementary_files_format_and_content: (1) chromosome
Supplementary_files_format_and_content: (2) nucleotide on Watson (+) strand
Supplementary_files_format_and_content: (3) position
Supplementary_files_format_and_content: (4) context (CG/CHG/CHH)
Supplementary_files_format_and_content: (5) dinucleotide-context (CA/CC/CG/CT)
Supplementary_files_format_and_content: (6) methylation-level = #_of_C / (#_of_C + #_of_T)
Supplementary_files_format_and_content: (7) #_of_C (methylated C, the count of reads showing C here)
Supplementary_files_format_and_content: (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

source_name: Male human fibroblasts (Coriell)

extract_protocol: The RRBS libaries were generated at previously described by Orozco et al. with minor modifications. DNA purifications for each enzymatic reaction was carried out using AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed using the Epitect kit (Qiagen) twice compared to manufacturer’s instruction to optimize the efficiency. Bisulfite-converted libraries were amplified using MyTaq Mix (Bioline) with the following program: (98° for 15 sec, 60° for 30 sec, 72° for 30 sec) 12 cycles, 72° for 5 min, 4°C storage.

value: Human fibroblasts


title: H3K27me3_ChIPSeq

city: Nanjing

first: Fang

last: Yuan

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argricultural University

data_processing:
The reads from ChIP-seq were aligned to rice genome (TIGR release 7) with 1 bp mismatch allowed using bowtie program. Only the reads mapped to a unique position of rice genome were included in the analysis.macs14 is the software for peak calling, parameter -s SAM, -t, --wig, --single, -g 3.8e+8 were used.
Supplementary_files_format_and_content: rice genome (TIGR release 7)

organism: Oryza sativa

source_name: leaves

growth_protocol: Rice cultivar ‘Nipponbare’ seedlings grown in green house for two weeks.

extract_protocol:
Commercial antibodies against H3K9me1(Millipore, 07-395) , H3K4ac(Millipore, 07-539),  H3K27me3(Millipore, 07-449), H3K27ac(abcam,ab4729), H3K9ac(Millipore, 07-352) and H3K9me3(Millipore, 07-442) were used in ChIP experiments. Construction of ChIP-seq libraries was according to the protocol of “preparing samples for ChIP sequencing of DNA” provided by Illumina. Briefly, ChIPed DNA was end repaired using ‘End-It DNA End Repair Kit’ (Epicentre, ER0720). The ‘dA’ base was then added to the 3’ ends of the blunt-ended DNA fragments using Klenow fragment (3’-5’exo-) (NEB, M0212S). Linker for single read was ligated to the DNA molecules with ‘dA’ overhang using LigaFast kit (Promega, M8221). After 2% agarose gel running with TAE buffer, the gel region containing about 150-300 bp DNA was excised for adapter ligated DNA size selection. The adapter modified DNA fragments were enriched by PCR and purified by running 2% agarose gel in TAE buffer for isolation of DNA fragments in the range of 200-300 bp. The purified DNA sample was ready for Illumina sequencing after quality validation.
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Leaves of two-week old rice cultivar ‘Nipponbare’ seedlings grown in green house were collected and ground into fine powder in liquid nitrogen. The resulting powder was suspended in nuclear isolation buffer (NIB: 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, 40% Glycerol, pH 7.5) and followed the standard protocol for nuclei isolation.

tag: cultivar

value: Nipponbare

value: Seedling

tag: developmental stage

value: two-week old

tag: antibody

value: H3K27me3(Millipore, 07-449)


title: H3K9ac_ChIPSeq

value: H3K9ac(Millipore, 07-352)


title: H3K4ac_ChIPSeq

value: H3K4ac(Millipore, 07-539)


title: H3K27ac_ChIPSeq


title: H3K9me3_ChIPSeq

value: H3K9me3(Millipore, 07-442)


title: RRBS_3S-5F-4_ESC_p30onSNL

description: 3S-5F-4 ESC p30onSNL

source_name: Undifferentiated female human induced pluripotent stem cells

value: Human induced pluripotent stem cells grown on SNL-feeders


title: RRBS_WIBR3_ESC_p10_rep1

description: WIBR3 ESC p10 rep1

source_name: Undifferentiated female human embryonic stem cells

value: Human embryonic stem cells


title: RRBS_K-3F-2_ESC_p26onSNL

description: K-3F-2 ESC p26onSNL


title: RRBS_ESI03_RA10d_p25

description: ESI03 RA10d p25

source_name: Differentiated female human embryonic stem cells

value: Human embryonic stem cells differentiated for ten days with retinoic acid


title: RRBS_WIBR2_ESC_p15_rep1

description: WIBR2 ESC p15 rep1


title: RRBS_WIBR2_ESC_p15_rep2

description: WIBR2 ESC p15 rep2


title: RRBS_H9_cardiac_p40_rep2

description: H9 cardiac p40 rep2

value: Cardiomyocytes differentiated from human embryonic stem cells


title: RRBS_ESI03_ESC_p24

description: ESI03 ESC p24


title: RRBS_H7_RA10d_p22

description: H7 RA10d p22


title: RRBS_K-3F-1_ESC_p15onSNL

description: K-3F-1 ESC p15onSNL


title: RRBS_WIBR3_ESC_p10_rep2

description: WIBR3 ESC p10 rep2


title: RRBS_H9_ESC_p38_rep2

description: H9 ESC p38 rep2


title: H3K9me1_ChIPSeq

value: H3K9me1(Millipore, 07-395)


title: RRBS_UCLA17_ESC_p15

description: UCLA17 ESC p15


title: RRBS_UCLA14_ESC_p23_rep1

description: UCLA14 ESC p23 rep1


title: RRBS_H7_ESC_p21

description: H7 ESC p21


title: RRBS_NHDF17914

source_name: Female human fibroblasts (Lonza)


title: RRBS_ESI02_RA10d_p69

description: ESI02 RA10d p69


title: RRBS_UCLA10_ESC_p10

description: UCLA10 ESC p10

source_name: Undifferentiated male human embryonic stem cells


title: RRBS_H9_ESC_p38_rep1

description: H9 ESC p38 rep1


title: RRBS_ESI02_ESC_p68

description: ESI02 ESC p68


title: RRBS_UCLA14_ESC_p23_rep2

description: UCLA14 ESC p23 rep2


title: RRBS_UCLA9_cardiac_p15_rep1

description: UCLA9 cardiac p15 rep1


title: RRBS_UCLA9_ESC_p13_rep2

description: UCLA9 ESC p13 rep2


title: RRBS_UCLA9_RA10d_p14

description: UCLA9 RA10d p14


title: RRBS_UCLA9_cardiac_p15_rep2

description: UCLA9 cardiac p15 rep2


title: RRBS_UCLA9_ESC_p13_rep1

description: UCLA9 ESC p13 rep1


title: RRBS_UCLA5_RA10d_p26

description: UCLA5 RA10d p26


title: RRBS_UCLA4_cardiac_p15_rep2

description: UCLA4 cardiac p15 rep2


title: RRBS_UCLA5_ESC_p25

description: UCLA5 ESC p25


title: RRBS_UCLA4_RA10d_p14

description: UCLA4 RA10d p14


title: RRBS_UCLA8_RA10d_p14

description: UCLA8 RA10d p14


title: RRBS_H9_cardiac_p40_rep1

description: H9 cardiac p40 rep1


title: RRBS_UCLA8_ESC_p13

description: UCLA8 ESC p13


title: RRBS_UCLA4_ESC_p13_rep2

description: UCLA4 ESC p13 rep2


title: RRBS_UCLA4_ESC_p13_rep1

description: UCLA4 ESC p13 rep1


title: RRBS_UCLA3_ESC_p14

description: UCLA3 ESC p14


title: RRBS_UCLA3_RA10d_p15

description: UCLA3 RA10d p15


title: RRBS_UCLA1_cardiac_p15

description: UCLA1 cardiac p15


title: RNA-seq_UCLA9_ESC_p15_SE

description: UCLA9 ESC p15 SE

data_processing:
RNA-seq library reads were mapped to the hg19 reference genome and gene annotation using tophat-2.0.4 (Trapnell et al., 2009) calling bowtie-0.12.8 (Langmead et al., 2009)
HTSeq (Anders et al., 2014) was used to perform gene counts
Genome_build: hg19
Supplementary_files_format_and_content: Tab seperated value spreadsheet of reads counts per gene (rows) for each sample (columns)

extract_protocol:
as described in paper
as described in paper


title: RNA-seq_UCLA8_ESC_clone3_SE

description: UCLA8 ESC clone3 SE


title: RNA-seq_UCLA9_ESC_p16_SE

description: UCLA9 ESC p16 SE


title: RRBS_UCLA1_RA10d_p14

description: UCLA1 RA10d p14


title: RNA-seq_UCLA8_ESC_clone2_SE

description: UCLA8 ESC clone2 SE


title: RNA-seq_UCLA8_ESC_p13_SE

description: UCLA8 ESC p13 SE


title: RNA-seq_UCLA8_ESC_p1_SE

description: UCLA8 ESC p12 SE


title: RRBS_UCLA1_ESC_p13

description: UCLA1 ESC p13


title: RNA-seq_UCLA8_ESC_clone23_SE

description: UCLA8 ESC clone23 SE


title: RRBS_UCLA9_neural_p14

description: UCLA9 neural p14

value: Neural cells differentiated from human embryonic stem cells


title: RNA-seq_UCLA3_ESC_SE

description: UCLA3 ESC SE

extract_protocol: as described in paper


title: RNA-seq_UCLA4_ESC_SE

description: UCLA4 ESC SE


title: RNA-seq_UCLA5_ESC_SE

description: UCLA5 ESC SE


title: RNA-seq_UCLA2_ESC_SE

description: UCLA2 ESC SE


title: RRBS_UCLA4_cardiac_p15_rep1

description: UCLA4 cardiac p15 rep1


title: RNA-seq_UCLA1_ESC_SE

description: UCLA1 ESC SE


title: RNA-seq_GM0227_p10

description: GM0227 p10

source_name: Human male fibroblasts

value: Human male fibroblasts


title: RNA-seq_ESI03_ESC_p24_rep1

description: ESI03 ESC p24 rep1


title: RNA-seq_H9_cardiac_p40_rep2

description: H9 cardiac p40 rep2


title: RNA-seq_H9_cardiac_p40_rep1

description: H9 cardiac p40 rep1


title: RNA-seq_ESI02_ESC_p68_rep2

description: ESI02 ESC p68 rep2


title: RRBS_UCLA2_ESC_p10

description: UCLA2 ESC p10


title: RNA-seq_ESI02_ESC_p68_rep1

description: ESI02 ESC p68 rep1


title: RNA-seq_UCLA9_cardiac_p15_rep2

description: UCLA9 cardiac p15 rep2


title: RNA-seq_UCLA9_cardiac_p15_rep3

description: UCLA9 cardiac p15 rep3


title: RNA-seq_H9_ESC_p38_rep2

description: H9 ESC p38 rep2


title: RNA-seq_UCLA9_cardiac_p15_rep1

description: UCLA9 cardiac p15 rep1


title: RNA-seq_H9_ESC_p38_rep1

description: H9 ESC p38 rep1


title: RNA-seq_UCLA9_ESC_p13_rep3

description: UCLA9 ESC p13 rep3


title: RNA-seq_UCLA8_ESC_clone10_SE

description: UCLA8 ESC clone10 SE


title: RNA-seq_UCLA4_cardiac_p15_rep2

description: UCLA4 cardiac p15 rep2


title: RNA-seq_UCLA4_cardiac_p15_rep1

description: UCLA4 cardiac p15 rep1


title: RNA-seq_UCLA9_ESC_p13_rep1

description: UCLA9 ESC p13 rep1


title: RNA-seq_UCLA4_cardiac_p15_rep3

description: UCLA4 cardiac p15 rep3


title: RNA-seq_UCLA9_ESC_p13_rep2

description: UCLA9 ESC p13 rep2


title: RNA-seq_UCLA1_cardiac_p15_rep1

description: UCLA1 cardiac p15 rep1


title: RNA-seq_UCLA8_ESC_p13_rep2

description: UCLA8 ESC p13 rep2


title: RNA-seq_UCLA4_ESC_p13_rep1

description: UCLA4 ESC p13 rep1


title: RNA-seq_NHDF17914_p5

description: NHDF17914 p5

source_name: Human female fibroblasts

value: Human female fibroblasts


title: RNA-seq_UCLA1_ESC_p13_rep3

description: UCLA1 ESC p13 rep3


title: RNA-seq_UCLA4_ESC_p13_rep3

description: UCLA4 ESC p13 rep3


title: RNA-seq_UCLA1_ESC_p13_rep2

description: UCLA1 ESC p13 rep2


title: RNA-seq_UCLA4_ESC_p13_rep2

description: UCLA4 ESC p13 rep2


title: U937-LT-2

city: Ansan

first: Se Kye

last: Kim

state: GYOENGGI-DO

address: 55 Hanyangdaehak-ro

department: Molecular and Life Science

country: South Korea

institute: Hanyang University ERICA

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the TopHat (version 2.0.10) software based on reference genome sequence (Mus musculus UCSC mm10) and the differential gene expressed values of each sample were calculated by Cufflinks(v2.2.1)
the number of reads mapped to gene ID features were counted using HTSeq v0.6.1.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: U937_LeTx treated

growth_protocol: Cells were seeded in 100 mm poly-L-lysine coated cell culture plate in RPMI medium containing 10% FBS (catalog # 26140), 100 IU/ml penicillin and 10 µg/ml streptomycin (catalog # 15140) from Invitrogen (CA, USA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C. The medium was changed every 2-3 days. Cells were sub-plated and used for further experiments.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with anthrax lethal toxin (1 μg/ml) for 24 hrs, and washed with RPMI medium to remove any residual toxins.

tag: cell line

value: human promonocytic lymphoma cell line

tag: treated with

value: LeTx (1 μg/ml) for 24 hrs


title: U937-Cont-2

value: none (control)


title: U937-Cont-1


title: A549-LT-2

source_name: A549_LeTx treated

value: human lung carcinoma cell line


title: A549-Cont-2


title: U937-LT-1


title: A549-Cont-1


title: RNA-seq_UCLA8_ESC_p13_rep1

description: UCLA8 ESC p13 rep1


title: Small RNA-seq Proliferating MEFs

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

data_processing: Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). For each run, reads were clipped from 3’ adapter sequences (requiring a minimum match of 10 nucleotides), using the fastx_clipper tool of the FASTX-Toolkit suite, discarding reads shorter than 15 nucleotides   (parameters: -a AGATCGGAAGAGCACACGTCT -l 25 -M 10 -Q 33). Reads were mapped to the reference miRBase v19 annotation using miRDeep2 (https://www.mdc-berlin.de/8551903/en/).  Processed data file in TXT format are provided (Columns: Mature miRNA ID, Reads count, Precursor miRNA ID, Total reads count (x2), Normalized counts (RPM)).

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were derived from 13.5d pregnant female mice and cultured in DMEM high glucose medium supplemented with 10% FBS

extract_protocol:
Cells were washed twice in 1X PBS, and lysed by addition of 1ml ice-cold TRIzol (Invitrogen). RNA integrity measurements were performed using Fragment Analyzer™ (Advanced Analytical). All samples had RNA Quality Number (RQN) greater than 9.8.
For Small RNA-seq library preparation, 1 μg of total RNA were used as input for the TruSeq Small RNA Library Prep Kit (Illumina), and libraries were prepared following manufacturer instructions

value: Mouse Embryonic Fibroblasts


title: RNA-seq Starved MEFs (2h Serum induction)

data_processing: Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference mouse mm9 assembly, using Tophat v2 (parameters: --bowtie1 -a 5). Provided BEDGraph files have been generated using Wiggles.

extract_protocol:
Cells were washed twice in 1X PBS, and lysed by addition of 1ml ice-cold TRIzol (Invitrogen). RNA integrity measurements were performed using Fragment Analyzer™ (Advanced Analytical). All samples had RNA Quality Number (RQN) greater than 9.8.
For RNA-seq library preparation, 2 μg of total RNA were used as input for the TruSeq RNA Library Prep Kit v2 (Illumina), and libraries were prepared following manufacturer instructions

treatment_protocol: Cells were starved in 0.2% FBS for 48h, and induced for 2h with 20% FBS


title: A549-LT-1


title: RNA-seq Starved MEFs (0.5h Serum induction)

treatment_protocol: Cells were starved in 0.2% FBS for 48h, and induced for 0.5h with 20% FBS


title: RNA-seq Starved MEFs (0h Serum induction)

treatment_protocol: Cells were starved in 0.2% FBS for 48h, and induced for 0h with 20% FBS


title: RNA-seq Starved MEFs (1h Serum induction)

treatment_protocol: Cells were starved in 0.2% FBS for 48h, and induced for 1h with 20% FBS


title: HEK_pxMARGI_rep2_2

first: Marcelo

last: Rivas

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: University of California San Diego

description:
Chimeric fragments from RNA-DNA interactions were retrieved. R1 and R2 reads correspond to RNA and DNA fragments, respectively. Thus, the paired-end files are not characterized by average insert size or standard deviation.
Processed data file: H9_P_pqvalues.poisson.txt

data_processing:
The first two bases of R1 reads were removed.
Duplicated paired-end reads were removed.
Reads containing linker sequences (found using FastQC) were trimmed.
Using only non-protein-coding genes (GTF from ENSEMBL GRCh38 release 84), we counted the RNA ends (R1 reads) per gene. For every gene, we determined the statistical significance of its RNA count under the null hypothesis that RNA ends are distributed proportionally to gene lengths. For a given gene x, we modeled the distribution of RNA counts with a Poisson function with parameter lambda=(count of RNA reads overlapping all genes)*(length of gene x)/(sum of all gene lengths). For each gene, P-values were computed as the probability of the gene RNA count being equal to or greater than its observed gene RNA count. The corresponding q-values were computed using the Bioconductor package qvalue.
Genome_build: GRCh38
Supplementary_files_format_and_content: *pqvalues.poisson.txt: Tab-delimited text files include raw counts. The files contain 7 columns: gene_id, gene_name (extracted from ENSEMBL GTF), biotype (extracted from ENSEMBL GTF), rna (observed RNA count), dna (observed DNA count), p-value (of observed RNA count), and q-value (of observed RNA count).

molecule: other

source_name: HEK cells

growth_protocol: HEK cells were cultured in Dulbecco's modified Eagle medium (DMEM; GIBCO 11960044) supplemented with 10% FBS, 2 mM Glutamax (GIBCO 35050061), and 5,000 U/ml penicillin/streptomycin (GIBCO 15070063), at 37 ºC with 5% CO2. H9 cells were cultured on matrigel (Corning 354277) coated plates and maintained in Essential 8 medium (GIBCO A1517001) at 37 ºC with 5% CO2.

extract_protocol:
The major steps of MARGI technologies are: crosslinking, isolation of nuclear material, protein biotinylation, genome fragmentation, RNA fragmentation, stabilization of proteins on streptavidin beads, end modification and RNA ligation, DNA ligation, reverse crosslinking, purification of RNA and DNA, removal of biotin from non-ligated linkers, pulldown of ligation products, reverse transcription, DNA denaturation, circularization and re-linearization, generation of sequencing library, and paired-end sequencing. See Extended Materials and Methods in published paper for details.
Sequencing library was generated by amplifying material using NEBnext Hi-fidelity PCR enzyme (New England Biolabs M0541S) with NEBnext multiplex oligos for Illumina sequencing (New England Biolabs E7335S) as the primers. Multiple test PCRs with 1 μL of sample and 10 μL reaction volume were run to identify the correct cycle number for the production run. The production PCR was run in a 50 μL reaction volume with 5 μL sample. After the PCR, size selection was performed using Ampure XP beads (Beckman Coulter A63880). Library between 200-2000 bp was selected. Library was run on a Bioanalyzer to determine the size distribution and then paired-end sequenced for 100 cycles at each end on Illumina HiSeq 2500 (PE100) or MiniSeq sequencers (PE150).

value: HEK

tag: protocol

value: pxMARGI


title: RNA-seq_UCLA1_ESC_p13_rep1

description: UCLA1 ESC p13 rep1


title: HEK_diMARGI_rep1_2

description:
Chimeric fragments from RNA-DNA interactions were retrieved. R1 and R2 reads correspond to RNA and DNA fragments, respectively. Thus, the paired-end files are not characterized by average insert size or standard deviation.
Processed data file: H9_I_pqvalues.poisson.txt

value: diMARGI


title: MDAMB134_genomic_input_DNA_2

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

data_processing:
Sequences were aligned to the human reference genome (GRCh37) using BWA version 0.7.12.
Duplicates were removed using Picard Tool version 1.47
Overlapping reads were clipped using clipOverlap tool from bamUtil repository version 1.0.14 with default parameters
SNPs were identified from gDNA samples using the Genome Analysis ToolKit 3.4-46 software across all gDNA samples simultaneously.
As per GATK recomendations, duplicated reads were removed and local realignment and base quality recalibration were employed prior to SNP  calling.
Called SNPs were filtered using a hard filtering criteria (QD < 2.0, FS > 60.0, MQ < 30.0, MQRankSum < -12.5, ReadPosRankSum < -8.0).
Allele-specific analysis was performed with BaalChIP R package (version 0.1.9) with the default parameters and options.
VariantAnnotaion (version 1.8.13) package in R was used to annotate ASB SNPs with respect to gene annotations
Genome_build: GRCh37
Supplementary_files_format_and_content: Information about the allele-specific SNPs identified in FAIRE-seq samples. The data contains SNP identifiers and chromosome coordinates according to dbSNP137 (columns "ID", "CHROM" and "POS"), the reference and alternative allele of each SNP (REF, ALT), information about which allele is specifically bound ("ASB_allele"), degree of the allele-specific imbalance as given by BaalChIP pipeline ("Allelic Imbalance"). The columns "GeneName" and "Location" correspond to SNP annotations relative to gene features (intron, coding, intergenic, etc).

source_name: MDAMB134 cells

growth_protocol: MDAMB134 and T47D human breast cancer cells were cultured in RPMI (Invitrogen) supplemented with 10% FBS and antibiotics. All cells were maintained at 37C, 5% CO2. All cell lines were from the CRUK Cambridge Institute biorepository collection. Cell lines were authenticated by short tandem repeat genotyping using the GenePrint 10 (Promega) system and confirmed to be mycoplasma free.

extract_protocol:
Cells were fixed for 10 mins in 1% formaldehyde in FCS-free medium, washed and frozen. Nuclei were isolated and sonicated in Diagenode Bioruptor using 300ul volumes in 1.5ml eppendorfs. MDAMB134 (3x107 cells/tube) and T47D (1.5x107 cells/tube). Sonication was performed for 20 cycles of 30s on/off. Sonicate was subjected to three consecutive phenol–chloroform–isoamyl alcohol (25:24:1) extractions and reverse cross-linked overnight. DNA was purified by ethanol precipitation and quantified by Quanti-iT. Genomic DNA was isolated using Qiagen DNeasy Blood and tissue Kit according to protocol.
DNA fragments are prepped for sequencing using the recommended protocol available for Angilent SureSelect-Illumina sequencing.

value: breast cancer cell line MDAMB134