title: Riboseq differentiating rep2

description:
mRNA footprints
Ribosome profiling


title: vitreous_mid_rep2

status: Public on May 17 2019

type: RNA

city: Davis

first: Zeljka

last: Smit-McBride

state: CA

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

country: USA

institute: University of California, Davis Eye Center

hyb_protocol: Affymetrix GeneTitan Chips were run at Genomics Services offered at Institute for Human Genetics at UCSF following manufactureres protocol.

scan_protocol: MicroRNA GeneChips were scanned using the Affymetrix GeneTitan Scanner as a part of Genomics Services offered at Institute for Human Genetics at UCSF.

data_processing: The data was analyzed with Expression Console (Affymetrix) and Transcriptome Analysis Console (Affymetrix) using GCRMA  miRNA arrays.

label: biotin

molecule: total RNA

organism: Macaca mulatta

label_protocol: The miRNA samples (10-20 nanograms) were labeled as probes using FlashTag kit.

growth_protocol: Primates were kept at UCRP at UC Davis Primate Center

extract_protocol: MiRNAs was isolated from each of the individual samples using Exiqon RNA isolation kit for fluids, quantified and quality checked on BioAnalyzer small RNA chips.

treatment_protocol: Animals were sacrificed with phenobarbitol injection by CNPRC stuff, eyes were disected, and aqueous and vitreous collected with syringe.  Blood was collected in purple top tube, spun down in Accuspin tube,  and plasma collected. Samples were stored at -80C till the RNA isolation step.

tag: exp. group

value: Group 3

tag: tissue

value: vitreous humor

tag: gender

value: female

tag: age


title: RNAseq differentiating rep4

type: SRA

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description: total RNA-seq

library_source: transcriptomic

data_processing:
Trim_galore! was used to remove small RNA adaters
TopHat2 (v 2.1.0) was used to align the reads to the hg38 reference genome
Ribo-seq reads were firstly aligned to a set of known rRNA and tRNAs (selected from the UCSC RepeatMasker tracks), followed by alignment of all unmapped reads to the reference genome.
FeatureCounts were used to count the number of reads per gene
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing counts for each gene and sample. For RNA-seq the exon counts, for Ribo-seq the coding sequence (CDS) counts are provided.

organism: Homo sapiens

source_name: H9 cells

growth_protocol: hESC were maintained in Essential 8 media (Thermo Fisher Scientific) on hESC-Qualified Matrigel (Corning) coated plates at 37°C, 5 % CO2. Cultures were dissociated in clumps using 0.5mM EDTA every 4 days and media was renewed daily.

extract_protocol:
mRNA footprints were prepared according to the ribosomal profilig protocol published by Ingolia et al., while total RNA was extracted using Trizol.
mRNA footprints were Ribozero treated (Illumina) and libraries were prepared using TruSeq Small RNA Preparation Kit (Illumina) according to manufacturer instructions. For RNA-seq, total RNA was treated with the RiboZero Magnetic Kit (Illumina) to remove ribosomal RNA. Libraries for sequencing were prepared using the NEB next Ultra Directional library prep kit for Illumina.

treatment_protocol: Differentiating hESC were cultured in MEF-conditioned KSR media plus 1uM retinoic acid in DMSO, while the control hESC population was maintained in MEF-conditioned KSR media completed with 4 ng/mL FGF2. Self-renewing cells were collected at Day 0, while differentiating cells at day 5 of treatment.

tag: cell type

value: human embryonic stem cells


title: Gata4 G295Ski/wt sample 3

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

description: valves

data_processing:
50 base paired end reads were performed on an illumina high seq 2500.
Fastq files were aligned to the mouse genome (mm9) using the STAR aligner version 2.4.0 in 2 pass mode using default parameters
Quality Control (QC) was performed on aligned files using RNASeQC and RSeQC to verify alignment quality.
Resulting BAM files were processed using cufflinks pipeline version 2.2.0 (cufflinks, cuffdiff, cuffnorm, and cuffquant) for gene expression and differential expression.
Principal component analysis identified a potential batch effect in sample KI2, as it did not group with other KI samples, and it was therefore removed from the study. All data is available for alll 6 samples for this study, with additional statistics that were performed without K2.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

organism: Mus musculus

source_name: E15.5 Outflow tract valves

extract_protocol:
Norgen Total RNA Extraction Kit
RNA TruSeq Stranded Total RNA LT with Ribo-Zero Gold Set A

value: outflow tract

value: embryonic day 15.5

tag: genotyp

value: Gata4 G295Ski/wt


title: Wildtype Sample 1

description: valves

value: Control


title: vitreous_mid_rep1


title: Riboseq self-renewing rep1

description:
mRNA footprints
Ribosome profiling


title: RNAseq differentiating rep3

description: total RNA-seq


title: Gata4 G295Ski/wt sample 2

description: valves


title: vitreous_old_rep1

value: Group 2


title: NC-1

city: chengdu

first: wang

middle: yu

last: jie

address: 211 Huimin Road, Wenjiang District, Chengdu

country: China

institute: Sichuan Agricultural University

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pig reference genome with stringent criteria (0 mismatch in the first 18bp)
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM), then standardized by the formula log2 (RPM+1), which allowed unbiased comparison among samples.
Genome_build: Genome database:mouse genome (assembly GCA_000001635.8); miRbase version: V21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

source_name: microRNA derived from negative control (NC) myotubes

growth_protocol: Murine skeletal muscle cell line C2C12 was cultured growth medium that contained high glucose DMEM supplemented with 10% fetal bovine serum, 100000 units/L of penicillin sodium, and 100 mg/L of streptomycin sulfate at 37 ℃ in a humidified atmosphere that contained 5% CO2.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000  Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

treatment_protocol: When the cells density reached about 80 % confluence, the C2C12 myoblasts were induced differentiation by placing  differentiation medium  that contained high glucose DMEM, 2% horse serum and present or absent 20 mM Guanidineacetic acid.

tag: strain background

tag: tissue source

value: myoblast

tag: cell line

value: Murine skeletal muscle cell line

tag: developmental stage

value: 6 days after differentiation


title: vitreous_old_rep2


title: AM-MSC

city: Guangzhou

first: Yi

last: Xiao

address: No. 253, Industrial Avenue, Haizhu District

institute: Southern Medical University

data_processing:
Quality control: Raw data (raw reads) in fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data. At the same time, Q20, Q30, and GC content in the clean data were calculated. All downstream analyses were based on clean data of high quality.
Read mapping to the reference genome: The reference genome and gene model annotation files were downloaded from the genome website( https://www.genome.gov/)
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene. Then, the FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis: Prior to DEG analysis, for each sequenced library, the read counts were adjusted using the edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. A corrected P-value of 0.05 and absolute fold-change of 2 were set as the threshold for significant differential expression.
GO and KEGG enrichment analysis: For DEGs, Gene Ontology (GO) enrichment analysis was implemented using the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected P values less than 0.05 were considered significantly enriched based on DEGs. The KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism, and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of DEGs in KEGG pathways.
Genome_build: HG38
Supplementary_files_format_and_content: counts

source_name: cell culture

growth_protocol: Umbilical Cord and Placenta derived cells were grown in MSC complete media and cultured in a carbon dioxide incubator at 37 ° C, 5% CO 2 , 95% humidity.

extract_protocol:
Total RNA was extracted using the Ambion PureLinkTM RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Amniotic membrane MSCs

tag: passages


title: CV-MSC

value: Chorionic villi MSCs


title: CM-MSC

value: Chorionic membrane MSCs


title: vitreous_yng_rep4

value: Group 1


title: Gata4 G295Ski/wt sample 1

description: valves


title: RNAseq differentiating rep1

description: total RNA-seq


title: UC-MSC

value: Umbilical cord  MSCs


title: vitreous_yng_rep3


title: D458 setd8-H4K20me1

city: Aurora

first: Rajeev

last: Vibhakar

state: CO

department: Pediatrics/Hematology/Oncology

institute: University of Colorado Anschutz Medical Campus

library_source: genomic

data_processing:
Bowtie2 was used to align the 150-bp paired-end sequencing reads to a reference human genome (hg19) downloaded from the UCSC Genome Browser.
Unmapped and non-uniquely mapped reads were removed, and PCR duplicate reads were removed using samtools version 1.5.
Peaks were called using MACS2 (v2.1.1.20160309)  with default parameters. Peak locations were further annotated according to the known genes in hg19 and 3000 bp of upstream and downstream of transcription start sites were considered as promoter regions using the R/Bioconductor package ChIPseeker
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files include peak files in track format with quantitative data

molecule: genomic DNA

source_name: medulloblastoma cell line D458

growth_protocol: D458 cell lines were cultured in DMEM (Gibco, Carlsbad, CA) supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (Gibco), 1× penicillin/streptomycin solution (Cellgro), and 1× L-glutamine (Cellgro). Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
genomic DNA was isolated by phenol/chloroform extraction and ethanol precipitation.  ChIP-DNA was quantified using the Qubit® dsDNA High Sensitivity Assay kit (Thermo Fisher).
Nugen Ovation Ultralow Library prep

treatment_protocol: Stable cell lines were established using gene specific mission shRNAs (Cat# 359304, 130139, 148268) or non-targeting control (Sigma-Aldrich, St. Louis, MO).  Cells were plated at 5x105 in a 6-well dish in growth medium containing 8µg/mL polybrene. Viral particles were added with 8µg/mL polybrene and incubated for 7 hrs.  Transduced cells were disaggregated, grown, and selected with 1µg/mL puromycin for 14 days.  Transformants were confirmed by qPCR and western blot.

tag: treatment

value: SETD8 80percent knockdown

tag: chip antibody

value: H4K20me1  Active Motif cat#39727

value: Brain


title: RNAseq self-renewing rep4

description: total RNA-seq

value: human embryonic stem cells


title: RNAseq self-renewing rep3

description: total RNA-seq


title: RNAseq self-renewing rep2

description: total RNA-seq


title: vitreous_yng_rep2

value: vitreous humor

value: female


title: ALAL1_RNAi_TNFalpha+_rep3

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

data_processing:
The generated BCL files were demultiplexed using bcl2fastq conversion software (version 2.17)
Quality control of the obtained reads was performed using fastqc and Trimmomatic
Filtered reads were mapped to the hg19 version using bowtie2
Read summarization was done with the featureCounts program and using the gencode.v19.hg19.gtf annotation
Differential gene expression was performed using the R package DESeq2.
Genome_build: hg19

source_name: HCC95 cells

growth_protocol: HCC95 cells were cultured at 37ºC in the presence of 5% CO2 using  RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% of pen strep

extract_protocol:
Total RNA from HCC95 cells was extracted using Maxwell® 16 Total RNA Purification Kit (Promega). Triplicates for each condition (ALAL-1 inhibition, TNFalpha treatment and controls) were performed. RNA quality was assessed using Agilent 2200 TapeStation.
RNA-seq libraries were prepared following the Illumina TruSeq Stranded mRNA Library Prep protocol

treatment_protocol: For ALAL-1 inhibition, 200,000 HCC95 cells per well were plated in a 6-well plate. The next day siRNAs at a final concentration of 30 nM siRNA were transfected using Lipofectamine 2000 (Invitrogen) following manufacturers protocol. The TNFalpha treatment was performed using a concentration of 10 ng/ml (R&D systems) for 4 hours.

value: HCC95 cells

value: TNFalpha treated

tag: RNAi

value: ALAL1 knockdown


title: ALAL1_RNAi_TNFalpha+_rep2


title: D458-IgG

value: SETD8 wild type

value: IgG


title: ALAL1_RNAi_TNFalpha+_rep1


title: vitreous_yng_rep1


title: D458-H4K20me1


title: RNAseq self-renewing rep1

description: total RNA-seq


title: ALAL1_RNAi_rep3

value: not treated


title: RNAseq differentiating rep2

description: total RNA-seq


title: D458-input

value: input


title: C16_Be2_IgD_pos

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw RNA sequencing reads were mapped to the hg19 version of the human genome using TopHat-v2.0.13 and Bowtie-v2.2.4
The sequencing coverage for all exons of each gene were counted using the samtools-v1.1 for each sample.  Raw read counts were normalized to Reads Per Kilobase of transcript per Million mapped reads (Rpkm) for all samples.
Genome_build: hg19
Supplementary_files_format_and_content: File containing rpkm values for all genes and rpm normalized BigWig files.

source_name: B cells

extract_protocol:
Total RNA was extracted with the Qiagn RNeasy Kit
300 ng of RNA was used as input for the KAPA Biosystems Stranded mRNA-seq kit with mRNA capture beads

tag: Sex

tag: sorting markers

value: CD19+ CD38mid CD27lo IgD+ CD4-

tag: be type

tag: igd status

value: Positive

tag: culture conditions

value: Purified naive B cells were co-cultured for 6 days in the presence of IL-2 (50U/ml) and IL-21 (10ng/ml) with allogeneic in vitro generated Th2 effectors (0.6x106 cells/ml, ratio 5B:1T) in Iscove's DMEM supplemented with penicillin (200 microg/ml), streptomycin (200migrog/ml), gentamicin (40microg/ml), 10% FBS, transferrin (50microg/ml) and insuline (5microg/ml).

tag: donor


title: ALAL1_RNAi_rep2


title: C16_Be2_IgD_neg

value: CD19+ CD38mid CD27lo IgD- CD4-

value: Negative


title: aqueous_mid_exp_rep4

tag: exp. group

value: Group 3

tag: tissue

value: aqueous humor

tag: gender

tag: age


title: aqueous_mid_exp_rep3


title: ALAL1_RNAi_rep1


title: aqueous_mid_exp_rep2


title: aqueous_mid_exp_rep1


title: apa_array: human_custom_library

city: Seattle

first: Georg

last: Seelig

state: WA

address: 3946 W Stevens Way NE

department: Electrical Engineering

institute: University of Washington

data_processing:
RNA sequences distinguished using designed barcodes
RNA mapped back to the full-length sequences and the isoform and site of polyadenylation recorded (python script)
RNA short and long isoform ratios calculated for each unique library sequence (python script)
Genome_build: Reporter sequences derived from Human build 37 GRCh37
Supplementary_files_format_and_content: array_noacut_score_50_metadata.csv.gz: tab-delimited file containing additional metadata such as constant sequence regions
Supplementary_files_format_and_content: array_noacut_score_50_unfiltered_cuts.mat.gz: matlab matrix file containing mapped RNA-seq read counts
Supplementary_files_format_and_content: array_noacut_score_50_unfiltered_mapped.csv.gz: tab-delimited file containing the processed designed sequences and clininical variant identifiers
Supplementary_files_format_and_content: array_noacut_score_50_unfiltered_misprime_mapped.csv.gz: tab-delimited file containing the processed and filtered designed sequences and APA measurements (potential misprimed sequences removed)
Supplementary_files_format_and_content: array_noacut_score_50_unfiltered.csv.gz: tab-delimited file containing the processed designed sequences and APA measurements

source_name: plasmid alternative polyadenylation reporter

growth_protocol: HEK293T cells were cultured on ECM-coated plates in Dubelco's DMEM media supplemented with FBS (5%), penicillin (.05%), and streptomycin (.05%)

extract_protocol:
RNA was extracted from transiently transfected cells 36-48 hours later using the NEB Monarch RNA Purification kit. The purified RNA was then polyA purified using the NEB PolyA Spin kit (magnetic-bead-based protocol).
Library specific priming sites were used to append Illumina adapter sequences and to amplify the library. Amplification was conducted in a light-cycler and samples removed early to minimize PCR bias.

treatment_protocol: Plated cells were seeded on ECM-coated plates and grown to ~90% confluency for 24-36 hours. Plasmid DNA was complexed with Lipofectamine 3000 reagent and transiently transfected.

tag: cell type

tag: molecule

value: reporter RNA


title: C16_Be1_IgD_pos

value: Purified naive B cells were co-cultured for 6 days in the presence of IL-2 (50U/ml) and IL-21 (10ng/ml) with allogeneic in vitro generated Th1 effectors (0.6x106 cells/ml, ratio 5B:1T) in Iscove's DMEM supplemented with penicillin (200 microg/ml), streptomycin (200migrog/ml), gentamicin (40microg/ml), 10% FBS, transferrin (50microg/ml) and insuline (5microg/ml).


title: aqueous_mid_rep3

value: female


title: C16_Be1_IgD_neg


title: Control_siRNA_TNFalpha+_rep3

tag: cell line

value: HCC95 cells

value: control


title: UC_Control_rep3

city: Montreal

first: Marika

last: Sarfati

state: Qc

address: 900 Rue St Denis

country: Canada

institute: CRCHUM

hyb_protocol: According to the manuafacture's sepcifications ( 65 degrees Celcius for 14 hours)

scan_protocol: nCounter Digital Analyzer (CCD camera). Barcodes were counted for each target molecule at High  Resolution

data_processing: NanoString nSolver Software

source_name: MLN, UC, Control

label_protocol: Reporter Codeset and Caputure ProbeSet

extract_protocol: NucleoSpin ® RNA extraction protocol

treatment_protocol: Sorted Th17 TEM cells (from mesenteric lymph nodes of Crohn's disease or ulcerative colitis patients undergoing surgical resection) were cultured in the presence or not of IL12 (20ng/mL) for 6 days.

tag: disease

value: Ulcerative colitis

tag: culture condition

value: Medium


title: UC_IL12_rep2

source_name: MLN, UC, IL12


title: UC_IL12_rep3


title: aqueous_mid_rep2


title: Control_siRNA_TNFalpha+_rep2

tag: treatment

value: TNFalpha treated


title: C15_Be2_IgD_pos


title: aqueous_mid_rep1


title: Control_siRNA_rep3

value: not treated

tag: RNAi


title: UC_Control_rep2


title: aqueous_old_rep4

value: Group 2


title: UC_IL12_rep1


title: C15_Be1_IgD_neg

tag: Sex


title: UC_Control_rep1


title: C15_Be2_IgD_neg

tag: sorting markers


title: Control_siRNA_TNFalpha+_rep1


title: Control_siRNA_rep2


title: aqueous_old_rep2


title: CD_Control_rep3

source_name: MLN, CD, Control

value: Crohn's disease


title: aqueous_old_rep3


title: C15_Be1_IgD_pos

value: CD19+ CD38mid CD27lo IgD+ CD4-

tag: be type

value: Positive


title: Control_siRNA_rep1


title: CD_IL12_rep3

source_name: MLN, CD, IL12


title: SON_summer_1

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

data_processing:
We used Tophat to map RNASeq reads to our dromedary genome assembly. Tophat’s default settings are optimised for the human genome, so we first adjusted these settings according to the genome of interest. We adjusted this range of acceptable intron lengths by using gene models to estimate the distribution of intron lengths and by selecting a range of sizes that account for 99.9% of known introns. In the dromedary genome, more than 3,000 putative introns have lengths that fall below while none are longer than 100,000; our final range was set to 8–52,000. We used HTSeq to generate read counts from each BAM file and used bespoke scripts to merge the counts into tables for DE prediction using DESeq and edgeR. Significance testing is pairwise via Fisher's Exact Test which is optimal for experiments with low replicates.
Genome_build: PRJNA310822
Supplementary_files_format_and_content: .counts

organism: Camelus dromedarius

extract_protocol:
Each sample was then homogenized in 1ml Trizol and the aqueous phase separated with Chloroform. Purification relied on the RNeasyMiniKit (Qiagen) according to manufacturers protocol. Concentration and quality of RNA was determined using both Nano-drop and Agilent Bioanalyzer 2100 and samples with a R.I.N>8 were used for library construction.
Stranded total RNA libraries were prepared according to IlluminaTruSeq stranded total RNA sample preparation guide (April 2013, Rev D) for Illumina Paired-End Multiplex Sequencing (Source Bioscience, Nottingham, UK). Ribo-Zero gold kit was used to remove cytoplasmic and mitochondrial rRNA prior to fragmentation and priming for first and second strand cDNA synthesis. The 3’ ends of fragments were adenylated and adapters and indexes (for the multiplex barcoding) ligated. Libraries were then subject to further quality control prior to pools with a concentration of 8pM being loaded onto lanes of an Illumina flowcell and sequenced using 100bp Paired End runs. Each sample resulted in >35million reads.

treatment_protocol: Summer vs Winter

tag: season

value: summer

tag: sample type

value: supraoptic nucleus (SON)


title: C11_Be2_IgD_neg

value: male

value: CD19+ CD38mid CD27lo IgD- CD4-

tag: igd status

value: Negative

tag: culture conditions

value: Purified naive B cells were co-cultured for 6 days in the presence of IL-2 (50U/ml) and IL-21 (10ng/ml) with allogeneic in vitro generated Th2 effectors (0.6x106 cells/ml, ratio 5B:1T) in Iscove's DMEM supplemented with penicillin (200 microg/ml), streptomycin (200migrog/ml), gentamicin (40microg/ml), 10% FBS, transferrin (50microg/ml) and insuline (5microg/ml).

tag: donor


title: C11_Be2_IgD_pos


title: SON_winter_3

value: winter


title: CD_IL12_rep2


title: CD_Control_rep2


title: aqueous_yng_rep4

tag: exp. group

value: Group 1

tag: tissue

value: aqueous humor

tag: gender

value: female


title: C11_Be1_IgD_neg

value: Purified naive B cells were co-cultured for 6 days in the presence of IL-2 (50U/ml) and IL-21 (10ng/ml) with allogeneic in vitro generated Th1 effectors (0.6x106 cells/ml, ratio 5B:1T) in Iscove's DMEM supplemented with penicillin (200 microg/ml), streptomycin (200migrog/ml), gentamicin (40microg/ml), 10% FBS, transferrin (50microg/ml) and insuline (5microg/ml).


title: aqueous_yng_rep3

tag: age


title: C11_Be1_IgD_pos


title: aqueous_yng_rep2


title: MDA-MB-231-conditioned-medium, ruxolitinib, rep3

status: Public on May 16 2019

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
subread_experiment_1.txt
231CM.RUX.3

data_processing:
Illumina Casava software used for basecalling.
Read mapping was performed via Hisat2 (v 2.0.2-beta) using the human reference genome (Ensembl GRCh38 release 89) or mouse reference genome (Ensembl GRCm38 release 94) when appropriate.
Gene level quantification was completed using Subread featureCounts (v1.4.6).
Principal components analysis (PCA) was completed in R on the 500 most variable genes using the “prcomp” function with rlog transformed data. PCA revealed a clear outlier (231CM.RUX.1) that had severe sequencing problems (only 2 million reads mapped to genes and the most highly expressed genes were a group of RNA genes, suggesting that mRNA enrichment during library prep failed in this sample). This sequencing outlier was removed from any further analysis.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample

molecule: polyA RNA

source_name: Primary macrophages

growth_protocol: Human primary macrophages were derived from PBMCs isolated from Trima Cones obtained through the Memorial Blood Center. PBMCs were subjected to CD14+ enrichment via MACS LS columns and differentiated into macrophages. All cells were grown at 37°C and 5% CO2 and regularly checked for mycoplasma contamination.

extract_protocol:
Total RNA was collected using TriPure reagent (Roche) from primary human PBMC- derived macrophages after treatment.
RNA-seq libraries were created using TruSeq Stranded mRNA Library Prep Kit (Illumina) and were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary human PBMC- derived macrophages treated with MDA-MB-231 CM in the presence of DMSO or 0.5μM ruxolitinib or from STAT3fl/fl and STAT3cKO BMDMs.

value: macrophage

tag: genotype

value: wild type

tag: phenotype


title: MDA-MB-231-conditioned-medium, ruxolitinib, rep1

description:
subread_experiment_1.txt
231CM.RUX.1


title: CD_IL12_rep1

tag: disease

tag: culture condition


title: SON_winter_2


title: SON_summer_2


title: MDA-MB-231-conditioned-medium, vehicle, rep1

description:
subread_experiment_1.txt
231CM.DMSO.1


title: vehicle-conditioned-medium, ruxolitinib, rep1

description:
subread_experiment_1.txt
RPMI.RUX.1


title: MDA-MB-231-conditioned-medium, ruxolitinib, rep2

description:
subread_experiment_1.txt
231CM.RUX.2


title: MDA-MB-231-conditioned-medium, vehicle, rep3

description:
subread_experiment_1.txt
231CM.DMSO.3


title: aqueous_yng_rep1


title: MCF7-conditioned-medium, ruxolitinib, rep1

description:
subread_experiment_1.txt
MCF7CM.RUX.1


title: vehicle-conditioned-medium, vehicle, rep2

description:
subread_experiment_1.txt
RPMI.DMSO.2


title: vehicle-conditioned-medium, ruxolitinib, rep2

description:
subread_experiment_1.txt
RPMI.RUX.2


title: MCF7-conditioned-medium, vehicle, rep2

description:
subread_experiment_1.txt
MCF7CM.DMSO.2


title: CD_Control_rep1

value: Medium


title: vehicle-conditioned-medium, ruxolitinib, rep3

description:
subread_experiment_1.txt
RPMI.RUX.3


title: aqueous_old_rep1

value: Group 2


title: vehicle-conditioned-medium, vehicle, rep1

description:
subread_experiment_1.txt
RPMI.DMSO.1


title: MCF7-conditioned-medium, ruxolitinib, rep3

description:
subread_experiment_1.txt
MCF7CM.RUX.3


title: MDA-MB-231-conditioned-medium, vehicle, rep2

description:
subread_experiment_1.txt
231CM.DMSO.2


title: MCF7-conditioned-medium, vehicle, rep3

description:
subread_experiment_1.txt
MCF7CM.DMSO.3


title: vehicle-conditioned-medium, vehicle, rep3

description:
subread_experiment_1.txt
RPMI.DMSO.3


title: MCF7-conditioned-medium, vehicle, rep1

description:
subread_experiment_1.txt
MCF7CM.DMSO.1


title: HCT116 21.3 c1 rep2

city: Marseille

first: Bianca

middle: Habermann

last: Hermine

address: 163 Avenue de Luminy

country: France

institute: Aix-Marseille University, CNRS, IBDM UMR 7288, 13009 Marseille, France

data_processing:
After quality control, reads were mapped using TopHat2 (v 2.0.9, default settings) against the Human Genome (version hg19).
Differential expression (log2FC, p-value, q-value) was done with cuffdiff (v2.1.1, default settings) using the accepted_hits.bam file for each sample comparing wild-type to trisomic cell line.

source_name: HCT116 cell line trisomic for chr. 21 clone 1

growth_protocol: Cells were maintained in 10 cm dishes in Dulbecco’s Modified Eagle Medium (DMEM) at 37°C and 5% CO2. Culture medium was supplemented with growth factors from 10% fetal bovine serum (FBS) and 1% Penicillin/ Streptavidin to avoid bacterial growth and contamination.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
TruSeq RNA library preparation and Illumina HiSeq2500 sequencing with 25 million 150bp single reads per library were performed by the Max Planck-Genome-Center Cologne, Germany.

tag: cell type

value: human colon carcinoma cell line

tag: genotype/variation

value: aneuploidy:trisomy of chromosome 21

tag: cell line


title: HCT116 21.3 c3 rep1

source_name: HCT116 cell line trisomic for chr. 21 clone 3


title: RPE1H2B 21.3 c2 rep3

source_name: RPE1 cell line trisomic for chr. 21 clone 2

value: human retinal pigment epithelial cell line,  immortalized with hTERT

value: stable expression:H2B tagged with GFP, aneuploidy:trisomy of chromosome 21

value: RPE1 hTERT H2B


title: HCT116 21.3 c3 rep2


title: RPE1H2B wt rep3

source_name: RPE1 cell line wild-type

value: stable expression:H2B tagged with GFP


title: RPE1H2B 21.3 c2 rep2


title: HCT116 21.3 c3 rep3


title: RPE1H2B 21.3 c2 rep1


title: RPE1H2B wt rep1


title: HCT116 21.3 c1 rep3


title: HCT116 21.3 c1 rep1


title: HCT116 wt rep3

source_name: HCT116 cell line wild-type

value: wild-type


title: MCF7-conditioned-medium, ruxolitinib, rep2

description:
subread_experiment_1.txt
MCF7CM.RUX.2


title: HCT116 wt rep2


title: HCT116 wt rep1


title: SCAF4KO3_TT-Seq_rep2

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

description:
Nascent RNA
TT-Seq

data_processing:
Illumina bcl2fastq v1.8 software used for basecalling.
Sequenced reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 86 transcript annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4 plus Dox

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS (Clontech, 631106), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 100 μg/ml hygromycin, 15 μg/ml blasticidin.  Additionally, 100 ng/mL doxycycline was used to induce SCAF4 or SCAF8 rescue constructs where applicable.

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
Libraries were prepared using the strand-specific TruSeq total RNA kit (Illumina) using 5 min 65°C fragmentation incubation to anneal primers but to prevent further fragmentation of the samples.

treatment_protocol:
plus 100ng/mL doxycycline, 15 min 4-thiouridine pulse
Nascent RNA labelling by addition of 1 mM 4-thiourdine to cell media for 15 min prior to harvest

tag: crispr status

value: SCAF4 single KO


title: YRE1A: YAPC EV 1

city: San Francisco

first: Rushika

middle: M

last: Perera

address: 513 Parnassus Ave, HSW1321

department: Anatomy

institute: UCSF

data_processing:
tophat2 was used to align the reads to hg19
cuffdiff version 2.1.1 was used to calculate differential expression
Genome_build: hg19
Supplementary_files_format_and_content: Txt file includes FPKM values for each sample

source_name: PDA cell line

extract_protocol:
Cells were treated with Doxycycline in full growth media for 6 days. RNA was extracted using Qiagen RNA kit. 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

value: PDA cell line

value: human pancreatic cancer

tag: dox treatment

value: Yes

tag: gli2 expression

value: No

tag: plasmid

value: pRetroX-Tight-Puro- EV


title: YRE1B: YAPC EV 2


title: YRE2A: YAPC EV 3


title: YRG1B: YAPC GLI2 2

value: pRetroX-Tight-Puro- GLI2


title: SCAF4KO2_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 plus Dox


title: YRG2B: YAPC GLI2 3


title: SCAF4SCAF8dKO3_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 minus Dox

treatment_protocol:
wash out of GFP-rescue protein, 15 min 4-thiouridine pulse
Nascent RNA labelling by addition of 1 mM 4-thiourdine to cell media for 15 min prior to harvest

value: SCAF4 and SCAF8 double KO


title: RPE1H2B wt rep2


title: WT2_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 plus Dox

value: WT

value: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8


title: SCAF8KO1_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 minus Dox

value: SCAF8 single KO


title: SCAF8KO2_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4 plus Dox


title: WT2_TT-Seq_rep1

description:
Nascent RNA
TT-Seq


title: SCAF4SCAF8dKO1_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4 minus Dox


title: SCAF8KO1_TT-Seq_rep1

description:
Nascent RNA
TT-Seq


title: SCAF4SCAF8dKO2_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4 minus Dox


title: SCAF8KO3_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4 plus Dox


title: SCAF4SCAF8dKO4_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF8 minus Dox


title: Riboseq_confluentHFF_rep2

city: Indianapolis

first: Michael

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

data_processing:
Library strategy: RNA ribosome footprints
for subconfluent samples: remove adapter sequences with CLIP tool from FASTX toolkit as implemented through usegalaxy.org platform
for confluent samples: remove adapter sequences with TrimGalore! (v0.4.3.1) as implemented through usegalaxy.org platform
alignment to human and Toxoplasma gondii genomes independently with HISAT2 (v2.1.0) using standard options as implemented through usegalaxy.org platform
feature counts obtained with htseq-count (v0.9.1) with standard options as implemented through usegalaxy.org platform
differential expression obtained with DESeq2 (v2.11.40.2) with standard options as implemented through usegalaxy.org platform
Genome_build: Toxoplasma gondii (ME49) v37 on ToxoDB.org and Homo sapiens v37 on HostDB.org
Supplementary_files_format_and_content: tab-delimited files with gene counts obtained with htseq-count

organism:
Homo sapiens
Toxoplasma gondii RH

source_name: Human Foreskin Fibroblasts

growth_protocol: parasites routinely subcultured in HFFs in DMEM supplemented with 1% heat-inactivated FBS w/o antibiotic; HFFs routinely subcultured in DMEM supplemented with 10% heat-inactivated FBS w/o antibiotics

extract_protocol:
cytoplasmic lysate was collected and an aliquot was immediately stored in Trizol for RNA-seq samples.  The rest was digested with RNaseI and monosomes were collecte by ultracentrifugation on a sucrose gradient. Ribosome-protected fragments (RFP) were purified after gel electrophoresis
RNA-seq and Ribo-seq samples of confluent samples were processed with the TruSeq Ribo Profile kit (Illumina) as per manufacturer. Subconfluent samples: total RNA was fragmented by alkaline hydrolysis. Fragments were purfied by gel electrophoresis. fragments were dephosphorylated, ligated at 5' end with barcoded adapter, rRNA removal with RiboZero mammalian kit (Illumina), phosphorylated, ligated at 3' end with SR-adapter, reverse transcribed & PCR with NEBnext barcoded adapters

treatment_protocol: HFFs were split, allowed to grow for 24 hours then infected with RH strain T. gondii for 24 hours in DMEM supplemented with 10% heat-inactivated FBS w/o antibiotic

tag: host cell type

value: human foreskin fibroblasts

tag: parasite

value: Toxoplasma gondii RH

tag: host growth

value: confluent


title: SCAF4KO3_TT-Seq_rep1

description:
Nascent RNA
TT-Seq

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4


title: SCAF4KO1_TT-Seq_rep2

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4 minus Dox

value: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4


title: SCAF4SCAF8dKO4_TT-Seq_rep1

description:
Nascent RNA
TT-Seq

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF8


title: SCAF4KO2_TT-Seq_rep1

description:
Nascent RNA
TT-Seq

value: SCAF4 single KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8


title: SCAF4SCAF8dKO3_TT-Seq_rep1

description:
Nascent RNA
TT-Seq


title: SCAF8KO2_TT-Seq_rep1

description:
Nascent RNA
TT-Seq

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4


title: SCAF4SCAF8dKO1_TT-Seq_rep1

description:
Nascent RNA
TT-Seq


title: YRG1A: YAPC GLI2 1

tag: tissue

value: PDA cell line

value: human pancreatic cancer

value: Yes


title: SCAF8KO3_TT-Seq_rep1

description:
Nascent RNA
TT-Seq

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4


title: WT1_TT-Seq_rep1

description:
Nascent RNA
TT-Seq

source_name: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4 plus Dox


title: SCAF4KO1_TT-Seq_rep1

description:
Nascent RNA
TT-Seq

treatment_protocol:
treatment protocol
Nascent RNA labelling by addition of 1 mM 4-thiourdine to cell media for 15 min prior to harvest


title: WT1_TT-Seq_rep2

description:
Nascent RNA
TT-Seq


title: SCAF4KO3_DRB.TT-Seq_40min_release

description:
Nascent RNA
DRB/TT-Seq

data_processing:
Illumina bcl2fastq v1.8 software used for basecalling.
Paired-reads were aligned to the GRCh38 version of the human genome using BWA-MEM v0.7.12 with default settings
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
NuGEN ultra low V2 kit (NuGEN)

treatment_protocol:
plus 100ng/mL doxycycline, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 40 min (including 10 min 1mM 4-thiouridine pulse)
3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)


title: WT2_TT-Seq_DRB.TT-Seq_40min_release

description:
Nascent RNA
DRB/TT-Seq


title: SCAF4SCAF8dKO2_TT-Seq_rep1

description:
Nascent RNA
TT-Seq

value: SCAF4 and SCAF8 double KO


title: SCAF8KO1_DRB.TT-Seq_30min_release

description:
Nascent RNA
DRB/TT-Seq

treatment_protocol:
wash out of GFP-rescue protein, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 30 min (including 10 min 1mM 4-thiouridine pulse)
3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)


title: SCAF4SCAF8dKO4_DRB.TT-Seq_30min_release

description:
Nascent RNA
DRB/TT-Seq


title: SCAF4SCAF8dKO4_DRB.TT-Seq_40min_release

description:
Nascent RNA
DRB/TT-Seq

treatment_protocol:
wash out of GFP-rescue protein, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 40 min (including 10 min 1mM 4-thiouridine pulse)
3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)


title: SCAF4SCAF8dKO4_DRB.TT-Seq_20min_release

description:
Nascent RNA
DRB/TT-Seq

treatment_protocol:
wash out of GFP-rescue protein, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 20 min (including 10 min 1mM 4-thiouridine pulse)
3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)


title: WT2_TT-Seq_DRB.TT-Seq_30min_release

description:
Nascent RNA
DRB/TT-Seq

treatment_protocol:
plus 100ng/mL doxycycline, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 30 min (including 10 min 1mM 4-thiouridine pulse)
3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)

value: WT


title: SCAF4KO3_DRB.TT-Seq_20min_release

description:
Nascent RNA
DRB/TT-Seq

treatment_protocol:
plus 100ng/mL doxycycline, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 20 min (including 10 min 1mM 4-thiouridine pulse)
3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)


title: SCAF4KO3_DRB.TT-Seq_10min_release

description:
Nascent RNA
DRB/TT-Seq

treatment_protocol:
plus 100ng/mL doxycycline, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 10 min (including 10 min 1mM 4-thiouridine pulse)
3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)


title: WT2_TT-Seq_DRB.TT-Seq_20min_release

description:
Nascent RNA
DRB/TT-Seq

value: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8


title: SCAF8KO1_DRB.TT-Seq_20min_release

description:
Nascent RNA
DRB/TT-Seq

value: SCAF8 single KO


title: WT2_TT-Seq_DRB.TT-Seq_10min_release

description:
Nascent RNA
DRB/TT-Seq


title: SCAF4SCAF8dKO4_DRB.TT-Seq_10min_release

description:
Nascent RNA
DRB/TT-Seq

treatment_protocol:
wash out of GFP-rescue protein, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 10 min (including 10 min 1mM 4-thiouridine pulse)
3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)


title: SCAF8KO1_DRB.TT-Seq_10min_release

description:
Nascent RNA
DRB/TT-Seq


title: SCAF8KO1_DRB.TT-Seq_40min_release

description:
Nascent RNA
DRB/TT-Seq


title: KO2_CD3CD28_IFNb

city: Philadelphia

first: Jonathan

last: Kotzin

state: PA

address: 421 Curie Boulevard, Biomedical Research Building II/III, Room 312

institute: UPenn

description: Morrbid_WT_KO_CD3CD28IFNb_DESeq2NormalizedCounts.txt

data_processing:
Sequenced reads were quality filtered and trimmed of adapters using Trimmomatic.
Reads were aligned to the GRCm38/mm10 genome using STAR v2.5.
Gene expression was quantified by counting the number of unique fragments mapped to genes using featureCounts.
DESeq2 was applied to identify differentially expressed genes and normalize gene counts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files of DESeq2 normalized gene counts

source_name: CD62Lhi CD44lo CD8+ T cells

extract_protocol:
Sorted CD62LhiCD44lo WT and Morrbid-/- splenic CD8 T cells were stimulated for 6 hours at 1x10^6 cells/mL using 1μg/mL plate-bound αCD3 (145-2C11), 1μg/mL soluble αCD28 (37.51) with and without 20ng/mL recombinant IFN-1 (Biolegend). RNA was harvested using a combination of TRIzol (Invitrogen) and RNeasy Mini columns (QIAGEN). TRIzol-chloroform extractions were precipitated with ethanol, applied to RNeasy Mini columns, and processed according to the manufacturer’s instructions.
Sequencing libraries were generated using the SMARTer Stranded Total RNA Sample Prep Kit Hi Mammalian kit (Takara) using 100ng of total RNA. Library quality and concentration were assessed by TapeStation and qPCR respectively.
Libraries were paired-end 75 base-pair sequenced on the NextSeq550 machine (Illumina).

tag: strain

value: Morrbid-/-

tag: type of stimulation

tag: length of stimulation


title: KO4_CD3CD28_IFNb


title: KO3_CD3CD28_IFNb


title: KO1_CD3CD28_IFNb


title: SCAF4KO3_DRB.TT-Seq_30min_release

description:
Nascent RNA
DRB/TT-Seq


title: ChIPseq_GIox_ZT8_rep1

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: GI ChIPseq at ZT8 replicate 1

data_processing:
For ChIP-seq data analysis, raw sequencing reads from the sequencer were demultiplexed and quality controlled with FastQC (v0.11.3). Reads with high quality were then aligned to the Arabidopsis reference genome (TAIR10) with Bowtie (v1.0.0) (Langmead et al., 2009), allowing only uniquely mapping reads with fewer than two mismatches, and duplicated reads were combined into one read.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

organism: Arabidopsis thaliana

source_name: GI ChIPseq at ZT8 replicate 1

growth_protocol: Wildtype, mutant, and transgenic lines used in this study were Arabidopsis thaliana ecotype Columbia 0 (Col- 0). gi-2 (Fowler et al., 1999), GIox (David et al., 2006), PIF5-HA (Lorrain et al., 2008), PIF4-Flash (Pedmale et al., 2016), pif3-1 (SALK_030753) (Kim et al., 2003), pif4-101 (Garlic_114_G06) (Lorrain et al., 2008), pif5-1 (SALK_087012) (Fujimori et al., 2004), pifQ (Leivar et al., 2008), and CCA1::LUC (Salome and McClung, 2005) have been previously described. pif3-1 and pifQ lines were obtained from the Arabidopsis Biological Research Center (ABRC) collection. The gi-2 mutation is a deletion (Δ670-677) that introduces a premature stop codon and is considered a null mutation predicted to encode a nonfunctional 114 aa polypeptide rather than the 1173 aa GI protein (Fowler et al., 1999).  Seeds were chlorine gas sterilized and plated on 0.5x Linsmaier and Skoog medium (LS, Caisson Laboratories) with 0.8% agar (Sigma). After stratification in the dark at 4 °C

extract_protocol:
Approximately 4 g of fresh weight whole seedlings were harvested at the indicated ZTs and cross-linked with 1%
ChIP-seq libraries were prepared with the NuGEN Ovation® Ultralow System as per manufacturer’s instructions.

value: whole seedlings

tag: genotype

value: GI overexpression (GIox;gi-2)

tag: ecotype

value: Columbia 0


title: WT4_CD3CD28_IFNb

value: wild type


title: WT3_CD3CD28_IFNb


title: WT2_CD3CD28_IFNb


title: WT1_CD3CD28_IFNb


title: KO2_CD3CD28

description: Morrbid_WT_KO_CD3CD28_DESeq2NormalizedCounts.txt


title: KO3_CD3CD28


title: ChIPseq_col_IP_ZT8_rep1

description: Col-0 ChIP seq at ZT8 replicate 1 - control


title: KO1_CD3CD28


title: WT3_CD3CD28


title: mESC_F123_P7_Control_Rep2

first: Jeffrey

middle: Michael

last: Alexander

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
Library strategy: 4C-seq
Reads were trimmed of the reading primer sequences using cutadapt (DOI: 10.14806/ej.17.1.200) with the following call: cutadapt -g
Reads were mapped to the mm9 genome using bowtie2 (PMID: 22388286) with default settings
BigWig files were created using deepTools (PMID: 27079975)  with the following call: deepTools bamCoverage -bs 1
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files for 4C-seq read density aligned to mouse genome

source_name: embryonic stem cells

growth_protocol: Embryonic stem cells were maintained in 2i + Lif media and grown at 37ºC with 5% CO2. Cells were passaged every 2 days.

extract_protocol:
Cells were crosslinked with 1% formaldehyde in PBS for 10 minutes at room temperature. Nuclei were isolated in lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630, 1X protease inhibitor). Chromatin was digested with 100 U of DpnII overnight at 37ºC. Next, samples were ligated with 2000 U of T4 DNA ligase for 4 hours at room temperature. After ligation, samples were incubated in 10% SDS with 1 mg/mL Proteinase K, follwed by reverse crosslinking through addition of 5M NaCl and incubating at 65ºC overnight. DNA was then linearized with 50U NlaIII overnight at 37ºC.
200ng of 4C template was used for PCR amplification for 30 cycles and 3-4 reactions were pooled together. Primers were designed to include Illumina adaptor sequences as well as barcodes derived from Illumina's TruSeq adaptors. PCR products were then purified using dual SPRI bead selection to select 120-1000bp fragments. Library concentrations were quantified using the KAPA qPCR system.

value: F1 hybrid 129/Castaneus

value: Embryonic stem cell

tag: Sex

value: Female

value: 129/CastEiJ F1 hybrid

value: Mouse embryonic stem cell


title: mESC_F123_P7_Control_Rep1


title: WT2_CD3CD28


title: 129_Cast_ESC_Sox2_SCR_CymRGFP_TetRtdTom_Rep2

value: Sox2-8CcuO/+; Sox2-117TtetO/+; Tg(epB-UbC-CymRGFP-DEx2); Tg(epB-CAG-TetRtdTom-DEx4)


title: 129_Cast_ESC_Sox2_SCR_CymRGFP_TetRtdTom_Rep1


title: 129_Cast_ESC_Sox2_SCR_Rep2

value: Sox2-8CcuO/+; Sox2-117TtetO/+


title: 129_Cast_ESC_Sox2_SCR_Rep1


title: WT_ischemia_3

first: Wayne

middle: W

last: Hancock

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: Affymetrix GeneChip Hybridization Wash and Stain Kit (PN:  900720) protocol was used for all hybridization, wash and staining steps.  Fragmented and labeled cDNA (130 μL at 25 ng/μL) were hybridized for 17 hr at 45° C to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays (PN: 902119).

scan_protocol: Chips were washed and stained on an Affymetrix Genechip Wash Station 450 using the FS450_0002 protocol and scanned on the Affymetrix GeneChip Scanner 3000. *.cel files were generated for analysis using Affymetrix GeneChip Command Console v3.2.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (GeneChip™ Mouse Gene 2.0 ST Array), and array data were analyzed using Transcriptome Analysis Console 4.0 software (ThermoFisher Scientific).

source_name: Renal cortex tissue

label_protocol: Sense-strand single-stranded cDNA was prepared from 150 ng of total RNA using the Ambion WT Expression Kit (PN:  4411974).  Both cRNA and cDNA were assessed using UV absorbance.  5.5 μg of single-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (PN: 900671).

growth_protocol: Female CreERT2 B6 mice (8-12 weeks old, 18-25 g) and HDAC2fl/fl-CreERT2 mice were housed in the CHOP animal facility. Conditional gene deletion was achieved by tamoxifen administration (100 mg/kg IP daily for 5 days, Sigma-Aldrich) with a 7-day recovery period after last administration before experimentation.

extract_protocol: RNA was isolated using RNeasy kits (QIAGEN). Total RNA was assessed by UV absorbance and all had 260/280 nm ratios above 1.7.  Additionally, samples were run on the Agilent RNA 6000 Nano chip and all had RINs in the 8.0 range.

treatment_protocol: To induce warm ischemia, Mice were anesthetized with pre-warmed pentobarbital sodium (65 mg/kg IP). Immediately after loss of a righting reflex, they were placed on a heated surgical pad (37 °C) in a temperature-controlled operative apparatus.  Core body temperature was continuously measured and maintained at 37.0  0.5 °C. Using an operating microscope, an abdominal midline incision was made, and the left renal pedicle exposed and clamped for 28 min with a microvascular clip (Roboz Surgical Instrument Company). After the clamp was released, the right kidney was removed and the abdomen closed. Animals were injected subcutaneously with 100 ml/kg of warm saline after the operation to assist in maintenance of hydration, and kept in an incubator (37 °C) from the time of anesthesia until completely awake.

value: Renal cortex tissue

value: Wild type ERT2cre

tag: treatment

value: 4h after ischemia


title: stat3ko, no-treatment, rep1

description:
subread_experiment_2.txt
STAT3_Cre_pos_Ctrl_1

source_name: Bone marrow derived macrophages

value: macrophage

value: STAT3 fl/fl c-fms-iCre

tag: phenotype

value: STAT3 knockout


title: HDAC2_3

value: no ischemia


title: HDAC2_ischemia_3


title: WT_2


title: WT1_CD3CD28

tag: genotype/variation


title: WT_3


title: HDAC2_ischemia_2


title: stat3wt, no-treatment, rep3

description:
subread_experiment_2.txt
STAT3_Cre_neg_Ctrl_3

value: STAT3 fl/fl

value: STAT3 wild type


title: WT_ischemia_2


title: HDAC2_1


title: HDAC2_ischemia_1


title: stat3ko, no-treatment, rep2

description:
subread_experiment_2.txt
STAT3_Cre_pos_Ctrl_2


title: WT_1


title: stat3wt, no-treatment, rep2

description:
subread_experiment_2.txt
STAT3_Cre_neg_Ctrl_2


title: HDAC2_2


title: stat3ko, no-treatment, rep3

description:
subread_experiment_2.txt
STAT3_Cre_pos_Ctrl_3


title: stat3wt, no-treatment, rep1

description:
subread_experiment_2.txt
STAT3_Cre_neg_Ctrl_1


title: Prrc2a RIP rep2

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: Prrc2a RIP rep2

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
For Prrc2a RIP-seq, the target binding regions of Prrc2a were identified using MACS2 software (version 2.0.10)ref with default options except for --nomodel. A stringent cutoff threshold for false discovery rate (FDR) < 0.05 was used to obtain high-confidence binding regions of Prrc2a.
Genome_build: mm10
Supplementary_files_format_and_content: txt, binding peaks for Prrc2a

source_name: mouse brain

extract_protocol:
For Prrc2a RIP-seq, three 4-weeks-old C57BL/6J male mice brains were dissected and placed in 10 ml lysis buffer (150mM NaCl, 10mM HEPES pH 7.6, 2mM EDTA, 0.5% NP-40, 0.5mM DTT, 1:100 protease inhibitors cocktail, 400Uml-1 RNase inhibitor). The tissues were cut and homogenated by homogenizer (Precellys Evolution, Bertin Technologies, Paris, France) and then the lysate was incubated on ice for 30 min. Lysates were centrifuged at 13000 rpm for 60 min at 4 °C. Protein concentration was determined using Coomassie PlusTM Protein Assay Reagent (Thermo Scientific) and diluted to final concentration at 4.0 mg/ml. Leave some tissue lysate as input.15 ml lysate were subjected to preclear with 12 mg normal goat IgG and 150 ml protein G magnetic beads at 4 °C for 2h. Following removal of the beads, lysates were incubated with 250 ml of protein G magnetic beads conjugated 20 mg Prrc2a antibody (Sc-78859, Santa Cruz) overnight at 4 °C with rotation. The beads were collected and washed eight times with 1 ml ice-cold NT2 buffer (200mM NaCl, 50mM HEPES pH 7.6, 2mM EDTA, 0.05% NP-40, 0.5mM DTT, 400Uml-1 RNase inhibitor). Then the beads resuspended in 500 ml 1×Micrococcal nuclease buffer with 2Uml-1 micrococcal nuclease and incubated 10 min at 37°C with rotation. Collected beads and washed two times with 1×PNK+EGTA buffer (50mM Tris-HCl pH 7.5, 20mM EGTA pH 8.0, 0.5% NP-40) following washed 2 times with NT2 buffer and once 1×PK buffer (100mM Tris-HCl pH 7.5, 50mM NaCl, 10mM EDTA, 0.2% SDS). Then the beads incubated with 4mg/ml proteinase K in 200 ml 1×PK buffer for 40 min at 50 °C. RNA recovered from supernatant by phenol-chloroform method further subjected rRNA removal. The purified RNA were used to generate the library using TruSeq stranded mRNA sample preparation kit (Illumina).For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
RNA was used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 (Illumina) in single-read or paired-read mode, creating reads with a length of 125 bp.

value: wild type

tag: age

value: 4 week

value: whole brain


title: WT_ischemia_1


title: 6KO

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

data_processing:
RNA-Seq libraries were prepared and sequencing was performed by the MD Anderson Cancer Center Sequencing and Microarray Facility
The raw reads were aligned to the Mouse reference genome build mm10, using Tophat2 RNASeq alignment software.
HTseq software is used to summarize the gene expression counts from Tophat alignment data after sorting the BAM files.
The raw counts are normalized and differential expression analysis is performed between KO and WT samples using the DEseq2 package.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Gene-Level Read Count files

source_name: Untreated KO

extract_protocol:
Fresh splenic cells were isolated from young WT and OTUB1-DKO mice (8-week old) and used for total RNA isolation with Trizol (Invitrogen), and subjected to RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: 6 to 8-week old

value: spleen

tag: cell type

value: splenic DCs


title: 7KO


title: 9-24h-WT

source_name: 24h-treated WT

value: WT

value: anti-CD3 (1ug/ml) plus anti-CD28 (1ug/ml) for 24 h


title: 7-24h-WT


title: NF6 input

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
Basecalls performed using CASAVA version 1.4
Sequencing reads were alligned to mm10 and hg38 using STAR tools
Low quality reads were filtered out and onlys readz >30 qc were rpcessed further
MeRIP peaks were identified using MeTPeak package
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Gene count files are provided as processed files, with read numbers detected and summed per gene for given sample.

source_name: heart tissue

extract_protocol:
RNA was extracted with Trizol reagent, treated with DNAse and cleaned up with Zymoresearch RNA clean-up and concentrator kit.
Libraries were constructed according to Illumina's protocol for TrueSeq stranded RNA library prep kit

tag: experimental condition

value: Normal Functionig Heart (NF)

tag: merip antibody

tag: sample type

value: RNAseq


title: Fto_TG_mouse_hippocampus_RNA-seq

description: Fto Tg RNA-seq

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.6. Differentially-expressed genes between control and Prrc2a knockout were determined  using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: txt; Reads count for each gene in WT and fto Tg sample

extract_protocol:
For RNA-seq, RNA was isolated from hippocampus sample from 4 weeks old Prrc2a flox/flox and Prrc2a flox/flox; Olig2-cre mice or 4 weeks old wt and Fto Tg micemice  using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen).  For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
Approximately 100ng of mRNA was used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp.

value: Fto Tg

value: hippocampus


title: NF5 IP

value: Antibody against N6-methyladenosine (Synaptic Systems, cat. no. 202 003)


title: 3WT

source_name: Untreated WT


title: Fto_WT_mouse_hippocampus_RNA-seq

description: wildtype RNA-seq


title: prrc2a WT mice_hippocampus_RNA-seq

description: prrc2a WT mice RNA-seq

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.6.Differentially-expressed genes between control and Prrc2a knockout were determined  using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: txt; Reads count for each gene in prrc2a WT and prrc2a::olig2-cre sample

extract_protocol:
For RNA-seq, RNA was isolated from hippocampus sample from 4 weeks old Prrc2a flox/flox and Prrc2a flox/flox; Olig2-cre mice using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen).  For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
Approximately 100ng of mRNA was used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp.

value: Prrc2a flox/flox


title: 2WT


title: NF5 input


title: prrc2a::olig2-cre_hippocampus_RNA-seq

description: prrc2a::olig2-cre RNA-seq

value: Prrc2a flox/flox;Olig2-cre


title: input rep1

description: input rep1

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
m6A peaks in two biological replicates m6A-immunoprecipitation sample were identified by MACS2 peak-calling software (version 2.0.10) with the corresponding input sample serving as control.
Genome_build: mm10
Supplementary_files_format_and_content: m6A peaks in two biological replicates.

extract_protocol:
RNA was isolated from mouse brain using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen) , fragmented and ethanol precipitated mRNA (6 μg) was incubated with 12 μg of anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer (150 mM NaCl, 0.1% NP-40, and 10 mM Tris-HCl [pH 7.4]) for 2 hr with rotatin at 4°C. The mixture was then immunoprecipitated by incubation with 50 μl protein-A beads (Sigma, P9424) at 4°C for an additional 2 hr. After being washed three times, bound RNA was eluted from the beads with 0.5 mg/ml N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted by Trizol. The remaining RNA was re-suspended in H2O and used for library generation with TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.
Approximately 100 ng of recovered RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp.

value: mouse brain


title: 1WT


title: m6A IP rep2

description: m6A IP rep2


title: m6A IP rep1

description: m6A IP rep1


title: NF4 input


title: input rep2

description: input rep2


title: 8-24h-WT


title: NF4 IP


title: NF6 IP


title: 11-24h-KO

source_name: 24h-treated KO


title: 12-24h-KO


title: Prrc2a cKO RNA-seq

description: Prrc2a knockout RNA-seq

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.6. Differentially-expressed genes between control and Prrc2a knockout were determined  using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: Reads count for each gene in control and prrc2a cKO sample

extract_protocol:
For RNA-seq, RNA was isolated from hippocampus sample from 4 weeks old Prrc2a flox/flox and Prrc2a flox/flox; nestin-cre mice using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen).  For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
Approximately 100ng of mRNA was used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp.

value: Prrc2a flox/flox; nestin-cre


title: NF3 input


title: 10-24h-KO


title: NF2 IP


title: NF3 IP


title: Prrc2a WT RNA-seq

description: wildtype RNA-seq

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.6. Differentially-expressed genes between control and Prrc2a knockout were determined using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: Reads count for each gene in control and prrc2a cKO sample


title: SCAF4KO3 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

data_processing:
Sequenced reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 86 transcript annotations.
Reads were aligned against GRCh38 and Ensembl release 86 transcript annotations using STAR v2.5.2a via the transcript quantification software RSEM v1.2.31.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4 plus Dox

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, 74104) according to the manufacture’s instruction including the on-column DNase treatment. 2μg total RNA was used for oligo(dT) purification.
TruSeq HT kit (Illumina)

treatment_protocol:
plus 100ng/mL doxycycline
None

tag: crispr status

value: SCAF4 single KO

tag: cell line


title: 5KO

tag: tissue


title: NF2 input


title: SCAF4SCAF8dKO4 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

treatment_protocol:
wash out of GFP-rescue protein
None

value: SCAF4 and SCAF8 double KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF8


title: ICM691 input

value: Ischemic Cardiomyopathy (ICM)


title: SCAF4KO2 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 plus Dox


title: SCAF4SCAF8dKO3 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 minus Dox


title: Prrc2a RIP rep1

description: Prrc2a RIP rep1

tag: strain

value: wild type

value: 4 week

value: whole brain


title: SCAF8KO1 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 minus Dox

value: SCAF8 single KO

value: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8


title: Irga409 under  Fe excess treatmen, biological rep2

city: Porto Alegre

first: Janette

middle: Palma

last: Fett

state: Rio Grande do Sul

address: Avenida Bento Gonçalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: Gene expression data from roots of BR-IRGA 409 plants exposed for three days to Fe excess condition

hyb_protocol: Target preparation, micro-chip hybridization, washing, staining, and scanning were carried out according to manufacturer's instructions (Affymetrix).

scan_protocol: The Affymetrix GeneChip Operating Software 1.2.1 was used for washing and scanning in the Fluidics Station 450 (Affymetrix) and the Scanner 3300 (Affymetrix), respectively.

data_processing: For further data analysis, the probe intensity files (.cel) were imported into the ArrayAssist software (Stratagene) and normalization and probe summarization were performed using the Robust Multichip Analysis algorithm, followed by variance stabilization.

organism: Oryza sativa Indica Group

source_name: BR-IRGA 409 plants

label_protocol: Five µg of total RNA were used as starting material for each sample, which were labeled using the one-cycle target labeling and control reagents (Affymetrix).

growth_protocol: Seeds from rice (Oryza sativa L. ssp. indica) cultivars EPAGRI 108 and BR-IRGA 409 were provided by the Rice Breeding Group from IRGA (Instituto Rio Grandense do Arroz, Brazil). The two genotypes are cultivated in southern Brazil and were previously characterized as tolerant (EPAGRI 108) and susceptible (BR-IRGA 409) to Fe toxicity (Silveira et al., 2007). Seeds were surface sterilized in ethanol 70% for two minutes, followed by NaClO4 1.5% for one minute, and then washed with abundant distilled water and germinated on moistened filter paper in Petry dishes. The seedlings were kept in the dark during the first 48 hours, transferred to 16h/8h day light regime (65 mol m- 2 s-1 of photosynthetic active radiation) at 28°C for two days and then transferred to pots with vermiculite, watered with nutrient solution consisted of 1.42 mM NH4NO3; 0.4 mM NaH2PO4; 0.5 mM K2SO4; 1.7 mM CaCl2.2 H2O; 1.7 mM MgSO4.7 H2O; 9.5 µM MnCl2.4 H2O; 0.07 µM (NH4)6Mo7O24.4H2O; 20 µM H3BO3; 0.16 µM ZnSO4.7H2O; 0.16 µM CuSO4.5 H2O; 35.6 µM FeCl3.6H2O and 0.07 mM citric acid (Yoshida et al., 1976). After 10 days, plants were transferred to hydroponic conditions, using the same nutrient solution, and after 10 more days plants were subjected to Fe excess (500 mg L-1 of iron) or control concentration (6.5 mg L-1), both using FeSO4 as the Fe source.

extract_protocol: For global gene expression analysis, highly purified total RNA was obtained using NucleoSpin RNA II (Macherey-Nagel) from roots of EPAGRI 108 and BR-IRGA 409 plants exposed for three days to control or Fe excess conditions, following manufacturer´s protocol.

treatment_protocol: Plants were subjected to Fe excess (500 mg L-1 of iron) or control concentration (6.5 mg L-1), both using FeSO4 as the Fe source, 20 days afeter germination, for three days, using a hydroponics system.

value: roots

value: BR-IRGA 409

value: three days to Fe excess condition


title: Irga409 under control solution, biological rep3

description: Gene expression data from roots of BR-IRGA 409 plants exposed for three days to control condition

value: control condition


title: Epagri108 under control solution, biological rep3

description: Gene expression data from roots of EPAGRI 108 plants exposed for three days to control condition

source_name: EPAGRI 108 plants

value: EPAGRI 108


title: Epagri108 under control solution, biological rep1


title: ICM585 IP

value: Antibody against N6-methyladenosine (Synaptic Systems, cat. no. 202 003)


title: Irga409 under control solution, biological rep1


title: Irga409 under control solution, biological rep2


title: Irga409 under  Fe excess treatmen, biological rep3


title: WT2 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 plus Dox

value: WT


title: Epagri108 under control solution, biological rep2


title: SCAF4SCAF8dKO2 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4 minus Dox


title: Seedling in darkness 37ºC 24 hours replicate 2

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

institute: IBMCP (UPV-CSIC)

hyb_protocol: Hybridization and slide washing were carried out with the Gene Expression Hybridization Kit and Gene Expression Wash Buffers, respectively

scan_protocol: Scanned on Agilent Technologies Scanner G2505B at a resolution of 5 microns per pixel,using the double scanning as Agilent’s recommended settings. Images were quantified using Agilent Feature Extraction Software (version 9.5.1)

data_processing: Interarray analyses were performed with the GeneSpring 12.1 software. To ensure a high-quality data set, control features were removed, and only features for which the ‘IsWellAboveBG’ parameter was 1 in at least three out of four biological replicates were selected

source_name: Seedling in darkness 37ºC 24 hours

label_protocol: 0.5 µg of total RNA 0.5 were amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit. Agilent’s Spike-In Kit was used to assess the labeling and hybridization efficiencies

growth_protocol: Seeds were sterilized by treatment with 70% ethanol for 20 min, commercial bleach (2.5% sodium hypochlorite) containing 0.05%  Triton X-100 for 10 min, and finally, four washes with sterile distilled water  . Seeds were sown placed onto Whatmann paper (Whatmann ) placed into Murashige and Skoog (MS) medium plates (Duchefa). Plates were kept in the dark at 4°C for 96 hours for stratification, and incubated during 8 hours in light in at 22°C to promote germination.

extract_protocol: Seedlings were frozen in liquid nitrogen, and grounded in mortars dipped in liquid nitrogen. Total RNA was extracted using the Quiagen Plant RNeasy Mini Kit followong the manufacturer´s recommendations.  Total RNA integrity was tested with the 2100 Bioanalyzer (Agilent).

treatment_protocol: Plates were transferred to darkness at 22ºC for 72 hours. At this moment plates were either kept at 22 ºC or transferred to 37º C. Seedlings were harvested at 0 and 24 hours with four biological replicates.

value: Whole seedling

tag: temperature

tag: time

value: 24 hours


title: Seedling in darkness 37ºC 24 hours replicate 3

tag: genotype


title: Irga409 under  Fe excess treatment, biological rep1


title: ICM585 input

value: RNAseq


title: SCAF8KO2 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4 plus Dox


title: DCM723 input

value: Dilated Cardiomyopathy (DCM)


title: SCAF8KO3 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4 plus Dox


title: DCM702 input


title: Seedling in darkness 37ºC 24 hours replicate 4


title: SCAF4SCAF8dKO1 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4 minus Dox

value: SCAF4 and SCAF8 double KO


title: DCM564 IP


title: Epagri108 under  Fe excess treatment, biological rep2

description: Gene expression data from roots of EPAGRI 108 plants exposed for three days to Fe excess condition


title: Seedling in darkness 22ºC 24 hours replicate 3

source_name: Seedling in darkness 22ºC 24 hours


title: Epagri108 under  Fe excess treatment, biological rep1


title: DCM589 IP


title: Seedling in darkness 22ºC 24 hours replicate 1


title: Seedling in darkness 22ºC 24 hours replicate 4


title: WT1 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4 plus Dox

value: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4


title: Control seedlings 0 hours replicate 4

source_name: Control seedlings with no heat treatment

value: 0 hours


title: DCM564 input

source_name: heart tissue


title: Seedling in darkness 22ºC 24 hours replicate 2


title: DCM702 IP


title: Control seedlings 0 hours replicate 1


title: DCM589 input


title: SCAF4KO3 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

value: SCAF4 single KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4


title: TAC8w33 polysome RNA

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 33) after 8 weeks (8w)

value: Polysomal RNAseq


title: SCAF4KO1 mRNA-Seq rep3

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4 minus Dox


title: TAC8w23 polysome RNA

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 23) after 8 weeks (8w)


title: TAC8w1744 IP

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1744) after 8 weeks (8w)


title: TAC8w17 polysome RNA

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 17) after 8 weeks (8w)


title: TAC8w1742 IP

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1742) after 8 weeks (8w)


title: PC3_1

city: Quebec City

first: Étienne

last: Audet-Walsh

state: Quebec

address: 2705 Boulevard Laurier, R-4714

institute: Centre de recherche du CHU de Québec - Université Laval

data_processing:
FastQC
Trimmomatic
FastQC
Kallisto
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files with RAWCOUNTS/TPM/FPKM values for each sample in two cell lines

source_name: PC3 cells

growth_protocol: Cells were maintened in RPMI 1640 supplemented with penicillin, streptomycin, sodium pyruvate, and 10% fetal bovine serum

extract_protocol:
RNA were purified using the RNeasy plus purification kit from QIAGEN.
NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina

treatment_protocol: After trypsinization, cells were plated in RPMI 1640 media with penicillin, streptomycin, sodium pyruvate, and 5% charcoal-stripped serum and without phenol red. Within the hour after seeding, cells were transfected with a non-targeted pool of siRNAs using Hiperfect transfection reagent according to the manufacturer's instructions.

tag: cell lines


title: SCAF4SCAF8dKO3 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8


title: PC3_2


title: SCAF4KO2 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 plus Dox


title: TAC8w1737 input

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1737) after 8 weeks (8w)


title: PC3_3


title: Control seedlings 0 hours replicate 2

value: Whole seedling


title: HL-60 CTR

city: Guangzhou

first: Xiaodan

last: Luo

address: NO.151 Yanjiang West Street, Yuexiu District

institute: The First Affiliated Hospital of Guangzhou Medical University

hyb_protocol: Each Slide was hybridized with 600ng Cy3‐labeled cRNA using Gene Expression Hybridization Kit (Cat#5188‐5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer ’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Processed_FC_data.txt contains genes with official GeneSymbol which displayed two-fold up-regulation or 0.5-fold down-regulation in expression in comparisons.

source_name: cell line, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One‐Color (Cat#5190‐2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer ’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596‐018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: HL-60 cells were subjected with infection of lentivirus expressing SATB1-shRNA1 and SATB1-shRNA2 or GV248 (empty vector). HL-60 SATB1-shRNA and HL-60-CTR cells were cultured with puromycin for 3 days to produce stable SATB1 knockdown cell line.

value: control


title: TAC8w1734 input

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1734) after 8 weeks (8w)

value: RNAseq


title: Epagri108 under  Fe excess treatment, biological rep3

value: roots

value: EPAGRI 108

tag: treatment

value: three days to Fe excess condition


title: 22rv1_3

source_name: 22rv1 cells


title: SCAF8KO1 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 minus Dox

value: SCAF8 single KO

value: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8


title: 22rv1_2


title: SCAF4SCAF8dKO4 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF8 minus Dox

value: SCAF4 and SCAF8 double KO


title: TAC8w1734 IP

value: Antibody against N6-methyladenosine (Synaptic Systems, cat. no. 202 003)


title: TAC8w1731 IP

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1731) after 8 weeks (8w)


title: TAC8w1727 IP

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1727) after 8 weeks (8w)


title: 22rv1_1


title: TAC8w1731 input


title: TAC8w1727 input


title: TAC8w1742 input


title: TAC8w1715 input

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1715) after 8 weeks (8w)


title: TAC8w1737 IP


title: TAC8w1715 IP


title: LNCaP_3

source_name: LNCaP cells

value: LNCaP


title: LNCaP_2


title: TAC8w04 polysome RNA

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 04) after 8 weeks (8w)

value: Polysomal RNAseq


title: TAC1w1714 IP

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1714) after 1 week (1w)


title: LNCaP_1


title: TAC1w1713 input

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1713) after 1 week (1w)


title: SCAF8KO2 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4


title: TAC1w1714 input

value: RNAseq


title: SCAF4KO3 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4 plus Dox

value: SCAF4 single KO


title: TAC1w1713 IP


title: WT1 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

value: WT

value: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4


title: SCAF4SCAF8dKO1 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq


title: TAC1w1712 IP

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1712) after 1 week (1w)


title: A549_TGFB_NUT_RNAseq_r1

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

description:
A549_tgfb_nutlin_RNAseq
rnaseq_tgfb.tsv

data_processing:
ChIP-Seq: Alignment done with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6, reads were quantified within peaks and normalized across samples
RNA-Seq: reads were mapped and analyzed by TopHat/Cufflinks RNA-seq analysis pipeline38 using Tophat version 2.1.0 and cufflinks version 2.1.1. Alignment was done against hg19 genome and hg19 RefSeq.gtf transcript annotations were used.
Genome_build: hg19
Supplementary_files_format_and_content: chipseq_tgfb.bed
Supplementary_files_format_and_content: rnaseq_tgfb.tsv

growth_protocol: Cells were passaged as at least twice post-thaw and used at a passage number of 6-14.  ~70% confluent plates were treated and harvested

extract_protocol:
ChIPseq lysates were clarified from sonicated nuclei and IPed with DO-1 anti-p53  antibody ( DO-1, Santa Cruz Biotechnology, SC-126X, Lot:G0115).   RNA samples were extracted with Trizol, purified on Zymo columns, and 500ng polyA selected.
DNA and mRNA libraries were prepared with standard illumina compatible protocols (NEBnext Kit)

treatment_protocol: Cells were treated with nutlin (5uM, 2hrs), and in some cases treated with TGFB for 5 days at 2.5ng/ml prior to nutlin treatment

tag: agent


title: TAC1w1712 input


title: TAC8w16 polysome RNA

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 16) after 8 weeks (8w)


title: TAC1w1710 input

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1710) after 1 week (1w)


title: TAC1w1709 IP

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1709) after 1 week (1w)

value: Antibody against N6-methyladenosine (Synaptic Systems, cat. no. 202 003)


title: A549_TGFB_RNAseq_r2

description:
A549_tgfb_RNAseq
rnaseq_tgfb.tsv

value: TGFB


title: TAC1w1711 IP

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1711) after 1 week (1w)


title: sham8w25 polysome RNA

value: sham treated (sham) mouse (ID 25) after 8 weeks (8w)


title: sham8w9 polysome RNA

value: sham treated (sham) mouse (ID 9) after 8 weeks (8w)


title: SCAF4SCAF8dKO4 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

value: SCAF4 and SCAF8 double KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF8


title: A549_TGFB_RNAseq_r3

description:
A549_tgfb_RNAseq
rnaseq_tgfb.tsv


title: TAC1w1711 input


title: WT2 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 plus Dox

value: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8


title: TAC1w1710 IP


title: A549_TGFB_RNAseq_r1

description:
A549_tgfb_RNAseq
rnaseq_tgfb.tsv


title: SCAF8KO1 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

value: SCAF8 single KO


title: sham8w18 polysome RNA

value: sham treated (sham) mouse (ID 18) after 8 weeks (8w)

value: Polysomal RNAseq


title: A549_NUT_RNAseq_r2

description:
A549_nutlin_2hrs_RNAseq
rnaseq_tgfb.tsv

tag: antibody

value: NUT


title: SCAF4KO2 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

value: SCAF4 single KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8


title: ICM691 IP

value: Ischemic Cardiomyopathy (ICM)


title: TAC1w1709 input

value: RNAseq


title: A549_NUT_RNAseq_r3

description:
A549_nutlin_2hrs_RNAseq
rnaseq_tgfb.tsv


title: SCAF4SCAF8dKO3 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 minus Dox


title: sham8w1748 input

value: sham treated (sham) mouse (ID 1748) after 8 weeks (8w)


title: SCAF4SCAF8dKO2 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4 minus Dox


title: sham8w20 polysome RNA

value: sham treated (sham) mouse (ID 20) after 8 weeks (8w)


title: A549_NT_RNAseq_r3

description:
A549_RNAseq
rnaseq_tgfb.tsv


title: sham8w1748 IP

value: Antibody against N6-methyladenosine (Synaptic Systems, cat. no. 202 003)


title: sham8w1735 IP

value: sham treated (sham) mouse (ID 1735) after 8 weeks (8w)


title: A549_NUT_RNAseq_r1

description:
A549_nutlin_2hrs_RNAseq
rnaseq_tgfb.tsv


title: SCAF8KO3 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4 plus Dox


title: A549_TGFB_NUT_RNAseq_r2

description:
A549_tgfb_nutlin_RNAseq
rnaseq_tgfb.tsv


title: A549_NT_RNAseq_r2

description:
A549_RNAseq
rnaseq_tgfb.tsv


title: sham8w1735 input


title: A549_NT_RNAseq_r1

description:
A549_RNAseq
rnaseq_tgfb.tsv


title: sham8w1725 IP

value: sham treated (sham) mouse (ID 1725) after 8 weeks (8w)


title: sham8w1743 IP

value: sham treated (sham) mouse (ID 1743) after 8 weeks (8w)


title: sham8w1743 input


title: sham8w06 polysome RNA

value: sham treated (sham) mouse (ID 06) after 8 weeks (8w)


title: SCAF4KO1 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

value: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4


title: sham1w1724 input

value: sham treated (sham) mouse (ID 1724) after 1 week (1w)


title: sham8w1732 input

value: sham treated (sham) mouse (ID 1732) after 8 weeks (8w)


title: sham1w1723 IP

value: sham treated (sham) mouse (ID 1723) after 1 week (1w)


title: DCM723 IP

value: Dilated Cardiomyopathy (DCM)


title: SCAF4KO3  RNAPII mNET-Seq rep2

description:
RNAPII 3'end associated RNA
mNET-Seq

data_processing:
Illumina bcl2fastq v1.8 software used for basecalling.
Reads were adapter trimmed using TrimGalore v0.4.4 with the following settings: “--paired --quality 20 -e 0.05 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a2 GATCGTCGGACTGTAGAACTCTGAAC --length 10”.
Paired reads were aligned against the GRCh38 genome using HISAT2 v2.04 in a strand-specific manner.
SAMtools was used to remove multi-mapping, duplicate and improperly paired reads.
The last base incorporated by the polymerase was isolated as the most 5' end of the second mate read and given the strand information of the first using the python script “get_SNR_bam.py” (https://github.com/tomasgomes/mNET_snr).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting single-bp BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

extract_protocol:
Cellular extracts were fractionated to generate nuclear and chromatin fractions as previously described (Nojima et al. 2016 Nature Protocols). Isolated chromatin was digested with MNase (40 U/mL, NEB, M0247) on a Thermomixer (1,400 rpm) at 37oC for 90 sec. MNase was inactivated by EGTA (25 mM) addition immediately after the reaction and soluble digested chromatin was collected by 13,000 rpm centrifuge for 5 min and diluted in NET-2 buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl and 0.05% (v/v) NP-40) and added to Pol II antibody-conjugated beads (MABI0601, MBL International). Immunoprecipitation was performed at 4oC for one hour. The beads were washed with 1 mL of NET-2 buffer 6 times and once with 500 mL of 1xPNKT (1xPNK buffer and 0.05 % Triton X-100) buffer in the cold room. The washed beads were incubated in 100 mL of PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/mL T4 PNK 3'phosphatase minus (NEB) on Thermomixer (1,400 rpm) at 37oC for 6 min. After the reaction beads were washed with 1 mL of NET-2 buffer and RNA was extracted with TRIzol (Thermo Fisher Scientific, 15596026). RNA was resolved on 8 % denaturing acrylamide 7 M urea gels for size purification. 35-100 nt fragments were eluted from the gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) and RNA was precipitated in 75 % Ethanol.
NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB)

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4


title: sham1w1723 input


title: SCAF8KO3 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

value: SCAF8 single KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4


title: A549_input_nt

description:
A549_chipseq_background
chipseq_tgfb.bed

value: input


title: A549_NT_nutin_p53cs_r2

description:
A549_p53_chipseq
chipseq_tgfb.bed

value: nutlin


title: SCAF4SCAF8dKO4  RNAPII mNET-Seq rep2

description:
RNAPII 3'end associated RNA
mNET-Seq

value: SCAF4 and SCAF8 double KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF8


title: sham1w1721 IP

value: sham treated (sham) mouse (ID 1721) after 1 week (1w)

value: Antibody against N6-methyladenosine (Synaptic Systems, cat. no. 202 003)


title: SCAF4SCAF8dKO2 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq


title: sham1w1719 IP

value: sham treated (sham) mouse (ID 1719) after 1 week (1w)


title: SCAF8KO2 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4 plus Dox


title: sham8w1732 IP


title: SCAF4SCAF8dKO1 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4 minus Dox


title: A549_input_tgfb

description:
A549_chipseq_background_tgfb
chipseq_tgfb.bed

value: TGFB


title: Control seedlings 0 hours replicate 3

source_name: Control seedlings with no heat treatment

value: Whole seedling

value: 0 hours


title: SCAF4SCAF8dKO4  RNAPII mNET-Seq rep1

description:
RNAPII 3'end associated RNA
mNET-Seq


title: MEFs transduced with wildtype YAP fused to mCherry (wtYAP-mCherry), replicate 2

city: New Haven

first: Amaleah

middle: Ann

last: Hartman

state: CT

address: 10 Amistad St.

department: Cell Biology

institute: Yale University

data_processing:
For data analysis, RNA-seq reads were aligned to the mouse genome mm10 using Tophat followed by differential gene expression analysis with Cufflinks in Galaxy.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs
Supplementary_files_format_and_content: DifferentiallyExpressedGenes

source_name: wtYAP04 MEF

growth_protocol: MEFs were cultured in standard MEF medium with 1 ug/mL Dox.

extract_protocol:
RNA was extracted with Trizol
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101)

treatment_protocol: Overexpression was achived by lentiviral mediated viral delivery

tag: transduction vector

value: YAP (wtYAP-mCherry)


title: sham8w1725 input

source_name: heart tissue

value: sham treated (sham) mouse (ID 1725) after 8 weeks (8w)

value: RNAseq


title: TAC8w1744 input

value: TAC (transverse aortic constriction) treated (TAC) mouse (ID 1744) after 8 weeks (8w)


title: MEFs transduced with wildtype YAP fused to mCherry (wtYAP-mCherry), replicate 1

source_name: wtYAP03 MEF


title: HL-60 SATB1-shRNA

tag: genotype/variation

value: SATB1 knockdown


title: sham1w1720 IP

value: sham treated (sham) mouse (ID 1720) after 1 week (1w)


title: sham1w1724 IP

value: sham treated (sham) mouse (ID 1724) after 1 week (1w)


title: WT1 mRNA-Seq rep1

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4 plus Dox

value: WT

value: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4