title: BSseq T1 pMORC6::MORC6-9xFLAG in morc6-3

first: C. Jake

last: Harris

address: Downing Street

department: Department of Plant Sciences

institute: University of Cambridge

description: 2-3 leaves from individual plant

data_processing:
Bisulfite-seq: Reads were aligned to the TAIR10 genome using BSMAP 2.89 (Xi and Li, 2009) allowing up to 2 mismatches and only retaining reads that mapped to one location. Methylation ratio are calculated by #C/(#C+#T) at C sites using the methratio.py script from BSMAP.
RNA-seq: Reads were mapped to the TAIR10 genome with TopHat2 2.0.9 (Kim et al., 2013) including the fr-firststrand parameter. Bigwig (.bw) tracks were generated by using 'bamCoverage' from the DeepTools suite, and are normalised by RPKM and parsed into 25bp bins.
Genome_build: TAIR10
Supplementary_files_format_and_content: .bw and Methylation ratio

organism: Arabidopsis thaliana

source_name: 3 week old leaf tissue

growth_protocol: 16 hours light 8 hours dark cycle

extract_protocol:
DNeasy Plant Mini kit (#69106),
Covaris sheared (500ng genomic DNA starting material from each), KAPA hyper prep kit (#KK8502), EZ DNA methylation lightning kit (#D5030). MyTAq HS mix for amplification (14 cycles)

tag: ecotype

value: 3 wk

tag: genotype

value: T1 pMORC6::MORC6-9xFLAG in morc6-3


title: Wildtype_TCDD_6

status: Public on Dec 31 2017

type: SRA

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

country: USA

institute: Woods Hole Oceanographic Institution

library_source: transcriptomic

data_processing:
Raw data files were trimmed using cutadapt
Trimmed reads were aligned to the genome using tophat2
Bam files were sorted using samtools
HTseq-count (union) was used to obtain the counts mapped to individual genes
edgeR was used to statistical analysis
Genome_build: GRCz10 version 84 (Danio_rerio.GRCz10.dna.toplevel.fa.gz/ Danio_rerio.GRCz10.84.gtf.gz)
Supplementary_files_format_and_content: HTseq-count data is in text format

molecule: total RNA

organism: Danio rerio

source_name: Wildtype TCDD exposed embryos

growth_protocol: ahrra null embryos were generated using zinc finger nuclease approach.

extract_protocol:
Total RNA from 72 hpf embryos was isolated using BioRad Aurum kit.
Unstranded libraries were constructed using Illumina's Truseq kit.

treatment_protocol: Wildtype and ahrra-null zebrafish embryos were exposed to either carrier control (0.01% DMSO) or 2nM TCDD for 1 hour at 6 hours post-fertilization. At the end of the exposure, embryos were thoroughly rinsed in fresh 0.3x Danieu's solution and maintained until 72 hpf.

tag: time point

value: 72 hpf embryos

tag: treatment

value: TCDD

tag: strain

value: Tupfel longfin


title: ISF.MLAC.20140808.008_S8

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

data_processing:
Fastq files were generated using the bcl to fastQ converter 2.17.
The raw reads were mapped to the mouse genome (mm10) using the STAR aligner version 2.4.0h1 in the two pass mapping mode
The mapped reads were quantified at the gene level using featureCounts version 1.4.6 using GENCODE VM4 comprehensive annotation
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with Gene symbol and Gene length in the first two columns, followed by 33 columns containing counts for each sample

organism: Mus musculus

source_name: wildtype_E15.5_whole kidney

extract_protocol:
RNA were extracted using QIAGEN RNeasy micro kit after snap-freezing fresh tissue in 1.5ml tube on dry ice.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: wildtype

tag: age

tag: Sex

value: male

tag: tissue

value: embyronic whole kidney

tag: batch


title: ISF.MLAC.20140808.007_S7


title: CO2 Deprivation 24h sample 1

city: Shanghai

first: Jianhua

last: Fan

address: 130 Meilong Road

country: China

institute: East China University of Science & Technology

data_processing:
Default parameters were used to pass reads using Illumina quality-control pipeline. All the filtered reads were trimmed. The processed sequence files were then mapped to the assembled genome by TopHat with a tolerance of up to 2 mismatches and 3 indels.
For each of the mRNA-seq datasets, the transcript relative abundance (TRA) was expressed as the numbers of aligned reads to annotated gene models using HTSeq method and then normalized to RPKM values
Genome_build: de novo assembly
Supplementary_files_format_and_content: text file of gene RPKM values. A file of FASTA sequences and the gff genome annotation are available on the series record.

organism: Auxenochlorella pyrenoidosa

source_name: whole cells_CO2 deprivation 24h

growth_protocol: Chlorella cells were cultivated photoautotrophically with 5% CO2.

extract_protocol:
the total RNA was isolated using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions.
The RNA samples were cleaned up using RNeasy columns (Qiagen, http://www.qiagen.com) following the manufacturer’s instruction. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: After five days cultivation, the broth was then transferred to air environment for CO2 deprivation (bubbled with air).


title: RNAseq T1 pMORC6::MORC6-9xFLAG in morc6-3

city: Cambridge

country: United Kingdom

description: 2-3 unopened floral buds from individual plant

source_name: unopened floral bud tissue

extract_protocol:
Direct-zol RNA miniprep kit (#R2050) including in-column DNase treatment
Each library is from a separate plant. 75ng total RNA was used as input for the TruSeq Stranded mRNA Library Prep Kit for Neoprep (NP-202-1001)


title: Wildtype_DMSO_3

source_name: Wildtype DMSO exposed embryos

value: DMSO


title: Wildtype_DMSO_2


title: RNAseq morc6-3 floral bud plant 2


title: ISF.MLAC.20140808.005_S5


title: RNAseq morc6-3 floral bud plant 3


title: ISF.MLAC.20140808.004_S4

source_name: heterozygous_E15.5_whole kidney

value: heterozygous

value: female


title: RNAseq WT floral bud plant 3

value: WT


title: ISF.MLAC.20140808.003_S3


title: RNAseq morc6-3 floral bud plant 1


title: ISF.MLAC.20140808.002_S2


title: Sample C (retired bee)

city: Yangzhou

first: Zhenguo

last: Liu

address: 88 South University Ave.

institute: Yangzhou University

data_processing:
Illumina GA Pipeline v1.5 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence,and filtered for reads with more than 10% unknown bases, then aligned to The DFCI Apis mellifera Gene Index (AMGI) by  SOAP2 aligner,no more than 2 mismatches are allowed in the alignment
Sequencing saturation analys, distribution of reads on reference genes, and coverage analysis were employed for the qulity control prupose.
The level of gene expression was calculated as RPKM (reads per kilobase transcriptome per million mapped reads), differentially expressed Genes (DEGs) were identified using an FDR≤0.001 (false discovery rate no greater than 0.05)
Cluster v3.0 and javaTreeview v1.1.1 were used forExpression pattern analysis of DEGs. Gene Ontology functional analysis was based on GO::TermFinder. KEGG (major public pathway-related database) is used in our pipeline to perform pathway enrichment analysis of DEGs for  further understand genes biological functions.
Genome_build: The DFCI Apis mellifera Gene Index (AMGI)
Supplementary_files_format_and_content: Excel files include RPKM values, discription, GO function, and Blastnr for each Sample

organism: Apis mellifera

source_name: Hypopharyngeal glands tissue

growth_protocol: Full-sister honey bees (Apis mellifera carnica Pollmann) produced by sexually mature virgin queens were artificially fertilized with sperm collected from an isolated, sexually mature drone using an artificial insemination instrument to minimize noise in the genetic background. Bees were left to develop age-matched adults after emergence from the comb in the apiaries of Yangzhou University, China.

extract_protocol:
Total RNA was extracted from the HGs of the samples (each pooled from 30 honey bees) using TRIzol reagent (Invitrogen, USA). A Qubit fluorometer (Invitrogen, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., USA) were used to determine the quality and quantity of the RNA. The mRNA was enriched using oligo (dT) magnetic beads, then fragmented into short fragments (approximately 200-700 nt) using fragmentation buffer (Invitrogen, USA). Double-stranded cDNA product was synthetized and purified .
sequencing adapters were ligated to the fragments, and the fragments were purified by agarose gel electrophoresis (AGE) and enriched by PCR amplification. The library products were sequenced using the Illumina HiSeqTM 2000 system.

value: Hypopharyngeal glands tissue

value: day 9 after emergence from the comb

value: Apis mellifera carnica Pollmann


title: Sample A (winter bee)

value: day 3 after emergence from the comb


title: ISF.MLAC.20140808.006_S6


title: osd1_2_MIR845_pollen

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

description: Small RNA

data_processing:
After de-multiplexing, 36-nt reads were pre-processed by trimming the 3’ adapter and filtering collapsed reads according to length and quality.
Filtered reads were mapped to the Arabidopsis TAIR10 genome annotation (or GFP transgene) with bowtie reporting all multi-mappers.
Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features

source_name: Pollen

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were always surface sterilized with sodium hypochlorite, sowed on Murashige and Skoog (MS) medium and stratified for 3 days at 4ºC. Seedlings were transplanted to soil two weeks after germination and grown under long day conditions at 22 °C.

extract_protocol:
Pollen was collected in 1.5mL eppendorf tubes by vortexing open flowers in pollen extraction buffer (PEB, 10 mM CaCl2, 2 mM MES, 1 mM KCl, 1% H3BO3, 10%) for 3 min, followed by filtration through a 30um mesh (Partec/Sysmex) and centrifugation at 5,000g for 1 min. Purification of pollen expressing the GFP-miR845b sensor in dcl1-5/+ and dcl1/+,dcl2/dcl4 mutants was performed by vortexing open flowers in 1 mL of PEB and filtering through a 30um mesh before FACS. Pollen population was identified in SSC/FSC scatter plots, and GFP fluorescence was analyzed by excitation with a 488nm laser and detected with a 530/30 bandpass filter. Pollen total RNA was extracted using Trizol LS reagent (Life Technologies) by vortexing with glass beads for 5 minutes, and concentrated with Direct-zol columns (Zymo Research).
Small RNAs were purified by running total RNA on acrylamide gels (15% polyacrylamide, 7M urea) and performing size selection of approximately 18 to 30-nt region using a small RNA ladder (Zymo Research). The small RNA fraction was isolated from acrylamide gel plugs by grinding with a plastic pestle in Trizol LS (Life Technologies), and concentrated using Direct-zol columns (Zymo Research). Libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina) following manufacturer instructions.

value: Pollen


title: RNAseq WT floral bud plant 2


title: GCE4_S4


title: Ler_MIR845_pollen

description: Small RNA


title: Sample B (spring bee)

value: day 6 after emergence from the comb


title: RNAseq WT floral bud plant 1


title: GCE3_S3


title: osd1_2_pollen

description: Small RNA


title: GCE2_S2


title: Ler_pollen

description: Small RNA


title: GCE1_S1


title: Cont4_S8


title: dcl2dcl4_FACS_pollen

description: Small RNA


title: Scale E16 RCAS-Zic1-deltaC, rep3

city: Los Angeles

first: Ping

last: Wu

state: CA

address: 2011 Zonal Ave HMR313A

department: Pathology

institute: University of Southern California

description:
Scale_E16_Zic1-dC
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

data_processing:
Prealignment QA/QC, adaptor sequence trimming, alignment of reads (TOPHAT 2, UCSC galGal4), and postalignment QA/QC were done in Partek Flow.
Partek Genomic Suite was used for RNA-seq read quantification, normalization and differentially expressed analysis.
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: E16_feather_scale_all_genes_RPKM.txt: Tab-delimited text file includes RPKM values for the complete set of genes for each sample.
Supplementary_files_format_and_content: E16_feather_scale_keratin_genes_RPKM.txt: Tab-delimited text file includes RPKM values for both differentially expressed and non-differentially expressed keratin genes for each sample.

organism: Gallus gallus

source_name: Scutate scale, E16, Zic1-deltaC misexpression

growth_protocol: Fertilized eggs.

extract_protocol:
Dissected tissue was extracted in Trizol reagent.
Libraries were prepared using Illumina TruSeq RNA Sample Preparation V2.

treatment_protocol: The gene misexpression was performed by injecting RCAS viruses to the amniotic cavity and hind limb of E3 chicken embryos, or by injecting RCAS plasmid followed by electroporation. For retinoic acid delivery, 30  g of retinoic acid was injected into the amniotic cavity at E9.

tag: breed

value: White Leghorn

value: scutate scale

tag: developmental stage

value: embryonic day 16

value: Zic1-deltaC misexpression


title: Cont3_S7

value: wildtype


title: Scale E16 RCAS-Zic1-deltaC, rep1


title: Cont2_S6


title: nrpd1a-3 SC

library_source: genomic

data_processing:
Paired end reads were treated as single end reads, preprocessed using Trimmomatic 45 to remove adapters, trim the first 10 nucleotides and split the read in half. Preprocessed C/T- and G/A-converted reads were mapped to C/T- and G/A-converted TAIR10 genome allowing two mismatches.
Perl and Python scripts were used to recover the sequence of each mapped read and calculate methylation at each individual cytosine covered by 3 or more reads.
Differentially methylated regions (DMRs) were defined as 100bp bins containing at least 4, 6 or 8 differentially methylated mCGs, mCHGs or mCHHs, respectively, and absolute methylation difference of 0.35. DMRs localizing 200bp of each other were merged.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files with cytosine methylation values (CG,CHG,CHH)

molecule: genomic DNA

source_name: Sperm cell nucleus

extract_protocol:
Pollen nuclei were isolated by FACS as previously described in Borges et al. 2012 BMC Plant Methods and Schoft et al. 2015 Plant Reproduction.
Approximately 50.000 nuclei were used to construct sequencing libraries of bisulfite-treated DNA using the Pico Methyl-Seq kit (Zymo Research), according to manufacturer instructions.

value: Sperm cell nucleus


title: dcl1dcl2dcl4_FACS_pollen

description: Small RNA


title: Cont1_S5

value: male

value: embyronic whole kidney


title: Ler:MIR845 VN

source_name: Vegetative nucleus

value: Vegetative nucleus


title: Scale E16 RCAS-Spry2, rep1

description:
Scale_E16_Spry2
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

source_name: Scutate scale, E16, Spry2 misexpression

value: Spry2 misexpression


title: ISF.MLAC.20140808.001_S1

value: heterozygous


title: Ler VN


title: Scale E16 RCAS-Spry2, rep2


title: 18_ZV105_5

city: New Haven

first: Akiko

last: Iwasaki

state: CT

address: 1 Gilbert St

institute: Yale

data_processing:
Basecalling was performed using the Illumina NextSeq 500  Real-time Analysis (RTA) v2 software
The raw reads of RNA-seq experiments were trimmed off sequencing adaptors and low quality regions by btrim (Kong, 2011).  The trimmed reads were mapped to mouse genome (GRCm38) by tophat2 (Kim et al., 2013).
After the counts are collected, the differential expression analysis was done by DEseq2 (Love et al., 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: .txt file showing normalized reads

molecule: polyA RNA

source_name: Placenta

extract_protocol:
Placentas were collected into Trizol. Trizol extraction followed by purification with Qiagen Rneasy kit was used to extract RNA.
cDNA libraries were prepared from RNA using NEB Ultra 1 library kit.

value: Placenta

value: Ifnar+/-

tag: infection

value: ZIKV ivag E5.5


title: Scale E16 RCAS-Sox18, rep2

description:
Scale_E16_Sox18
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

source_name: Scutate scale, E16, Sox18 misexpression

value: Sox18 misexpression


title: Scale E16 RCAS-Sox18, rep3


title: Ler SC


title: 17_ZV105_4


title: 25_ZV108_8


title: 23_ZV108_5


title: Scale E16 RCAS-Sox18, rep1


title: Scale E16 RCAS-Sox2, rep2

description:
Scale_E16_Sox2
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

source_name: Scutate scale, E16, Sox2 misexpression

value: Sox2 misexpression


title: nrpd1a-3 VN


title: 15_ZV105_2

value: Ifnar-/-


title: 14_ZV105_1


title: Scale E16 RCAS-Grem1, rep1

description:
Scale_E16_Grem1
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

source_name: Scutate scale, E16, Grem1 misexpression

value: White Leghorn

value: Grem1 misexpression


title: Scale E16 RCAS-Grem1, rep2

value: scutate scale

value: embryonic day 16


title: Scale E16 RCAS-Zic1-deltaC, rep2

value: Zic1-deltaC misexpression


title: 5_U20_8

value: Uninfected


title: Scale E16 RCAS-GFP control, rep2

description:
Scale_E16_GFP
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

source_name: Scutate scale, E16, GFP control

value: GFP control


title: Scale E16 RCAS-GFP control, rep1


title: Ler:MIR845 SC

value: Sperm cell nucleus


title: 6_U20_9


title: 2_U20_2


title: 22_ZV108_4


title: Scale E16 RCAS-beta-catenin, rep1

description:
Scale_E16_b-Cat
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

source_name: Scutate scale, E16, beta-catenin misexpression

value: beta-catenin misexpression


title: 20_ZV108_2


title: 19_ZV108_1


title: Scale E16 RA treated, rep2

description:
Scale_E16_RA
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

source_name: Scutate scale, E16, RA treated

value: retinoic acid


title: Feather E16 control, rep2

description:
Feather_E16
Processed data file: E16_feather_scale_all_genes_RPKM.txt
Processed data file: E16_feather_scale_keratin_genes_RPKM.txt

source_name: dorsal skin, E16

value: dorsal skin


title: 3_U20_3

value: Placenta


title: Scale E16 RA treated, rep1


title: Feather E16 control, rep1


title: 1_U20_1

value: Ifnar+/-


title: Scale E16 RCAS-Sox2, rep1


title: MeDIP_Hippocampal_neurons_4h_KCL_rep3

city: Freiburg

first: Henriette

last: Franz

address: Alberstr: 17

department: Anatomy and Cellbiology

country: Germany

institute: University Freiburg

description:
Name of company: 6_2577Albert_Hippo_KCl_5mC_i91
Hippocampal neurons were isolated at day E18.5, cultured for 11 days in vitro and then treated with or without 55mM KCL, then MeDIP-seq was performed

data_processing:
The  sequence reads identified by the Active Motif Sequencing Service (NextSeq 500, 75-nt single-end, flowcell AH1350BGXX) are mapped to the genome using the BWA algorithm with default settings.Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 150 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Active Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals). In locations where only one sample has an Interval, this Interval defines the Active Region.
Genome_build: mm10

source_name: hippocampal neurons

extract_protocol:
C57BL/6J (Janvier Labs, France) hippocampi of E18.5 embryos were dissected and collected in 15 ml Hanks’ Balanced Salt Solution (HBSS, PAA, Germany). After centrifugation (5min; 800xg) hippocampi were dissociated by adding 1ml 0.05% trypsin-ethylenediaminetetracetic acid (PAA) at 37°C for 15min. After adding 1ml of fetal bovine serum (FBS, Life Technologies) and 1ml of neurobasal (NB) medium supplemented as previously described (Vezzali R et al. 2016) samples were homogenized by repeated passages through a pipette tip. After 10min centrifugation at 1000Xg, cells were resuspended in complete NB medium containing 22µM L-glutamic acid (Sigma, Germany), counted, and seeded on poly-ornithine (0.1 mg/ml, Sigma) and laminin (1μg/ml, Sigma) coated plates. Medium change was performed every 96h by exchanging half of the volume of the medium with fresh NB medium with complements and AraC (1µg/ml for the first, and 0.5µg/ml for the second medium change, Sigma). At day in vitro (DIV) 11 cells were treated with 55mM KCl at 37ºC, 5%CO2 at different time points before harvesting.
The company Active motif processed the samples, constructed the library and analyzed the data.

treatment_protocol: samples treated or untreated with 55mM KCl

value: cultured hippocampal neurons

tag: differentiation state in vitro

value: 11 days


title: MeDIP_Hippocampal_neurons_4h_KCL_rep2

description:
Name of company: 4_2577Albert_Hippo_KCl_5mC_i89
Hippocampal neurons were isolated at day E18.5, cultured for 11 days in vitro and then treated with or without 55mM KCL, then MeDIP-seq was performed

growth_protocol: 1000Xg, cells were resuspended in complete NB medium containing 22µM L-glutamic acid (Sigma, Germany), counted, and seeded on poly-ornithine (0.1 mg/ml, Sigma) and laminin (1μg/ml, Sigma) coated plates. Medium change was performed every 96h by exchanging half of the volume of the medium with fresh NB medium with complements and AraC (1µg/ml for the first, and 0.5µg/ml for the second medium change, Sigma).


title: dG9a 12h

city: matsugasakihashigami tyo

first: Kohei

last: Shimaji

department: Applied biology

country: Japan

institute: Kyoto Institute of Technology

data_processing:
RNA-seq
We aligned the mRNA-seq reads to the reference Drosophila melanogaster genome sequence (UCSC dm6) using the TopHat (Kim et al. 2013) program version 2.1.0 with the option ‘--library-type fr-secondstrand’.
Cufflinks (Trapnell et al. 2013) (version 2.2.1) was then employed with the option ‘-u --library-type fr-secondstrand’ to assemble transcripts and to calculate fragments per kilobase of transcript per million mapped fragments (FPKM).
Differentially expressed genes were also identified using Cuffdiff in the Cufflinks program package.
Genome_build: UCSC dm6

organism: Drosophila melanogaster

source_name: 12 h starved

growth_protocol: Fly stocks were cultured at 25ºC on standard food.

extract_protocol:
RNAs were isolated using Trizol ® reagent (Invitrogen). The extraction procedures were repeated twice and samples were combined for the analysis. Isolated Isolated RNAs were used for comparison with Illumina mRNA-seq libraries using a TruSeq Stranded mRNA Sample Prep Kits (Illumina) according to the manufacturer’s instructions.
The obtained libraries were subjected to sequencing on a HiSeq 1500 system (Illumina) for 51 cycles.

treatment_protocol: Five days old adult flies were placed into vials including a piece of paper soaked with 1.0 mL PBS under non-crowded conditions (20 flies per vial) and were collected after 0 h and 12 h with each fly line.

value: 5 days old adult

tag: stress

value: 12 h starvation


title: dG9a 0h

source_name: 0 h starved

value: 0 h starvation


title: MeDIP_Hippocampal_neurons_4h_KCL_rep1

description:
Name of company: 2_2577Albert_Hippo_KCl_5mC_i87
Hippocampal neurons were isolated at day E18.5, cultured for 11 days in vitro and then treated with or without 55mM KCL, then MeDIP-seq was performed


title: 4_U20_4

value: Ifnar-/-


title: CS 0h

value: Canton S


title: MeDIP_Hippocampal_neurons_untreated_rep3

description:
Name of company: 5_2577Albert_Hippo_cont_5mC_i90
Hippocampal neurons were isolated at day E18.5, cultured for 11 days in vitro and then treated with or without 55mM KCL, then MeDIP-seq was performed


title: CS 12h


title: MeDIP_Hippocampal_neurons_untreated_rep2

description:
Name of company: 3_2577Albert_Hippo_cont_5mC_i88
Hippocampal neurons were isolated at day E18.5, cultured for 11 days in vitro and then treated with or without 55mM KCL, then MeDIP-seq was performed


title: Scale E16 RCAS-beta-catenin, rep2

value: White Leghorn

value: scutate scale

value: embryonic day 16


title: mDC-educated OT-I CD8 T Cells 72h 3

city: Chicago

first: Shann

middle: S

last: Yu

state: IL

address: 5640 S Ellis Ave, Eckhardt Research Center

department: PME-Immunoengineering Center

institute: University of Chicago

description: RNA isolated from OT-I cells with Qiagen Rneasy Plus kit, and poly-A selection with RT-PCR was used to select for mRNAs for creation of libraries for sequencing (Illumina TruSeq Stranded mRNA library prep kit).

data_processing:
FastQC (Babraham Bioinformatics, Cambridge, UK) - Sequence quality and contamination check
Read mapping and counting with HTSStation platform, which uses Bowtie2 algorithm.
Differential expression analysis (pairwise between all 7 conditions) performed using Bioconductor Limma.R package.
Adjusted p-values calculated with Benjamini-Hochberg multiple tsting adjustment.
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: PRJNA347820_Genes_Counts&RPKMs.xls is a list of RPKMs and raw counts for each of the 21 samples, following gene calling. PRJNA347820_Transcripts_Counts&RPKMs.xls is an array of RPKMs and counts for detected transcripts. All other files (provided as .txt) contain adjusted p-values and Log-Fold Changes for the pairwise comparison indicated in the filename (n = 3 per condition), based on either gene calling or raw transcripts.

source_name: CD8 splenocytes (neg selection) from OT-I mice

growth_protocol: OT-I cells were selected by negative magnetic selection of CD8 cells from whole spleen of an OT-I mouse. They were then co-cultured on a monolayer of flow cytometry-sorted lymphatic endothelial cells (LECs; podoplanin- and CD31- double-positive), which had been pre-pulsed with ovalbumin and washed prior to addition of OT-I cells at a ~10:1 T:LEC ratio. As a control, bone marrow-derived dendritic cells (DCs) were generated ia the Lutz protocol, and matured with LPS and pulsed with ovalbumin prior to addition of OT-I cells at the same ratio. Co-cultures proceeded for up to 3 days, and because LECs and DCs eventually adhere to the plates, non-adherent cells were removed and treated for sequencing.

extract_protocol:
Qiagen RNeasy Plus kit to isolate total RNA, which was then submitted to EPFL Gene Expression Core Facility for library preparation and sequencing. Their standard protocol involves poly-A selection and RT-PCR for selection of mRNA, and library preparation using the Illumina TruSeq mRNA library prep kit.
Illumina TruSeq mRNA library prep kit

value: OT-I


title: mDC-educated OT-I CD8 T Cells 72h 2


title: MeDIP_Hippocampal_neurons_untreated_rep1

description:
Name of company: 1_2577Albert_Hippo_cont_5mC_i86
Hippocampal neurons were isolated at day E18.5, cultured for 11 days in vitro and then treated with or without 55mM KCL, then MeDIP-seq was performed


title: mDC-educated OT-I CD8 T Cells 72h 1


title: mDC-educated OT-I CD8 T Cells 48h 1


title: mDC-educated OT-I CD8 T Cells 48h 3


title: mDC-educated OT-I CD8 T Cells 24h 3


title: mDC-educated OT-I CD8 T Cells 24h 2


title: LEC-educated OT-I CD8 T Cells 72h 3


title: LEC-educated OT-I CD8 T Cells 72h 2


title: mDC-educated OT-I CD8 T Cells 24h 1


title: TMU06(AA)_endosperm_sRNA_rep2

city: Nanjing

first: Wu

last: Jiao

address: 1 Weigang Road

institute: Nanjing Agricultural University

description: small RNA

data_processing:
Illumina CASAVA_v1.8.2 software used for basecalling.
Low-quality reads in the raw RNA-seq data were removed using NGSQCToolkit_v2.3
SlSl transcripts were assembled de novo using Trinity; RNA-seq reads of AA (TMU06) were mapped onto the A genome with TopHat, followed by cufflinks and cuffmerge to generate relative complete transcripts for every annotated gene. Orthologous regions between transcripts among A and Sl genomes were identified using BLAST.
The high-quality reads of AA, DD and AADD were mapped onto the A (T. urartu) and D (Ae. tauschii) genomes allowing two mismatches, while the reads of AA, SlSl and SlSlAA were aligned onto orthologous regions extracted from A and Sl transcripts allowing five mismatches, followed by Cufflink, Cuffmerge and Cuffdiff.
Raw small RNA sequence reads were parsed to remove 3’ adapters and collect 18-30-nt reads with cutadapt. Clean sRNA-seq data of AA, DD and AADD were mapped to A genome, D genome, and combined A and D genomes, respectively using bowtie without mismatch. Small RNA sequencing reads from AA, SlSl, SlSlAA and AADD were all mapped onto the A genome. After removing structural RNAs including ribosomal RNAs, transfer RNAs, snoRNAs, and snRNAs, sRNA reads were normalized by library size using the same weight for each matched locus (reads per 10 million reads, RPTM).
Genome_build: T. urartu (A genome, ftp://climb.genomics.cn/pub/10.5524/100001_101000/100050/A/Assembly/) and Ae. tauschii (D genome, ftp://climb.genomics.cn/pub/10.5524/100001_101000/100054/D/Assembly/); orthologous regions extracted from A and Sl genome transcripts
Supplementary_files_format_and_content: fpkm_tracking files were produced by Cuffdiff, and all other files were generated using in-house Perl scripts

organism: Triticum urartu

source_name: endosperm

extract_protocol:
Total RNA was isolated using miRVana kit (Ambion 1561) and Plant RNA Isolation Aid (Ambion 9690) to be used for RNA libraries and small RNA libraries.
RNA libraries and small RNA libraries were prepared for sequencing using standard Illumina protocols

value: 6 days after pollination


title: TMU38(AA)_endosperm_sRNA_rep1

description: small RNA


title: TMU06(AA)_endosperm_sRNA_rep1

description: small RNA


title: TMU38(AA)_endosperm_sRNA_rep3

description: small RNA


title: LEC-educated OT-I CD8 T Cells 72h 1


title: LEC-educated OT-I CD8 T Cells 48h 3


title: TMU38(AA)_endosperm_sRNA_rep2

description: small RNA


title: TMU06(AA)_endosperm_sRNA_rep3

description: small RNA


title: 24_ZV108_7

value: ZIKV ivag E5.5


title: TMU06(AA)_endosperm_mRNA_rep2

description: mRNA


title: TMU06(AA)_endosperm_mRNA_rep3

description: mRNA


title: LEC-educated OT-I CD8 T Cells 48h 2


title: TMU06(AA)_endosperm_mRNA_rep1

description: mRNA


title: Input_Hippocampal_neurons_pooled

description: Hippocampal neurons were isolated at day E18.5, cultured for 11 days in vitro and then treated with or without 55mM KCL, then MeDIP-seq was performed


title: mDC-educated OT-I CD8 T Cells 48h 2


title: LEC-educated OT-I CD8 T Cells 24h 2


title: TMU38(AA)_endosperm_mRNA_rep2

description: mRNA


title: TMU38(AA)_seedling-root_mRNA_rep3

description: mRNA

source_name: seedling root

value: 3-leaf stage


title: TMU38(AA)_endosperm_mRNA_rep1

description: mRNA


title: LEC-educated OT-I CD8 T Cells 48h 1


title: Naive OT-I CD8 T Cells 3


title: LEC-educated OT-I CD8 T Cells 24h 1


title: Naive OT-I CD8 T Cells 2


title: mir845 2n rep2

description: Small RNA

data_processing:
Reads were pre-processed by trimming the 3’ adapter and filtering collapsed reads according to length and quality.
Filtered reads were mapped to the Arabidopsis TAIR10 genome annotation with bowtie reporting all multi-mappers.
Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features

source_name: Pollen

extract_protocol:
Flowers were harvested in a beaker, covered with 9% sucrose solution and shaken vigorously for 5min to release pollen grains into the solution. The subsequent centrifugation- and filtering-steps were carried out in 9% sucrose solution. Total RNA was extracted using Trizol reagent (Ambion/ Life Technologies, USA) and glass beads (1.25-1.55 mm; Carl Roth).
10 μg of total RNA were run on a 14% TBE UREA Polyacrylamide gel for size selection. Gel slices containing RNA in the range of 17- to 25-nt were purified following the Illumina TrueSeq small RNA protocol for gel extraction. Libraries were constructed using the Illumina TruSeq Small RNA library preparation kit according to the manufacturer’s instructions.

value: Pollen


title: TMU38(AA)_seedling-root_mRNA_rep1

description: mRNA


title: Naive OT-I CD8 T Cells


title: mir845 2n rep1

description: Small RNA


title: Col VN

source_name: Vegetative nucleus

value: Vegetative nucleus


title: col_293457

data_processing:
FastQ files were processed and mapped to TAIR10 genome using SubRead, normalized by calculating the number of paired-end reads per kilobase of transcript per million of mapped reads (FPKM), and analyzed using R scripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt file with FPKM counts

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were always surface sterilized with sodium hypochlorite, sowed on Murashige and Skoog (MS) medium and stratified for 2-3 days at 4ºC. Seedling were transplanted to soil 2 weeks after germination.

extract_protocol:
Pollen was collected in 1.5mL eppendorf tubes by vortexing open flowers in pollen extraction buffer (PEB, 10 mM CaCl2, 2 mM MES, 1 mM KCl, 1% H3BO3, 10% Sucrose, pH 7.5) for 3 min (31), followed by filtration through a 30um mesh (Partec/Sysmex) and centrifugation at 5,000g for 1 min. Pollen was suspended in 50ul of PEB, immediately frozen in liquid nitrogen and stored at -80ºC until further use.
Libraries for RNA sequencing from Col-0 and Ler-0 pollen were prepared using rRNA-depleted total RNA samples and the ScriptSeq-v2 RNA-Seq Library Prep kit (Epicenter/Illumina), following manufacturer instructions.


title: ler_292304


title: mir845 1n rep2

description: Small RNA


title: Col SC

source_name: Sperm cell nucleus

value: Sperm cell nucleus


title: TMU38(AA)_endosperm_mRNA_rep3

description: mRNA


title: LEC-educated OT-I CD8 T Cells 24h 3


title: Seedlings [sRNA]

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

country: Switzerland

institute: ETHZ

description: Small RNA

data_processing:
Basecalling pipeline: HiSeq Control Software 2.2.38; RTA 1.18.61.0; CASAVA-1.8.2.
FASTQ file generation and demultiplexing and adapter removal were done by Fasteris.
Small RNA reads were aligned to the Arabidopsis thaliana genome using the ncpro-seq tools v1.5. (Parameters: -e 50 -a -m 5000 --best --strata --nomaqround -y)
Genome_build: TAIR10
Supplementary_files_format_and_content: *.processed.txt: Tab-delimited text files include distinct sequences and reads count values.

source_name: Seedlings

growth_protocol: Plants were grown for 2 weeks in soil in a 12hr/12hr light/dark cycle, then moved into a 16hr/8hr chamber.

extract_protocol:
RNAs were extracted by phenol/chloroform.
Extracted RNA was processed into sequencing libraries using adapted Illumina protocols and sequenced at Fasteris (http://www.fasteris.com , Switzerland) using the Illumina HiSeq sequencer.

tag: ecotype/background

value: wild type

value: Seedlings

tag: experiment type

value: small RNA-seq


title: Mono2 [RNA]

data_processing:
Library strategy: Ribo-Seq
Basecalling pipeline: HiSeq Control Software 2.2.38; RTA 1.18.61.0; CASAVA-1.8.2.
FASTQ file generation and demultiplexing and adapter removal were done by Fasteris.
Reads were trimmed with fastx_clipper and aligned with Tophat v2.0.11 and fpkm were calculated with Cufflinks v2.2.0.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_genes.fpkm_tracking: Cufflinks files include FPKM values.

source_name: Inflorescences

value: Inflorescences

value: monosomal ribosome profiling


title: Poly2 [sRNA]

description: Small RNA

data_processing:
Library strategy: Ribo-Seq
Basecalling pipeline: HiSeq Control Software 2.2.38; RTA 1.18.61.0; CASAVA-1.8.2.
FASTQ file generation and demultiplexing and adapter removal were done by Fasteris.
Small RNA reads were aligned to the Arabidopsis thaliana genome using the ncpro-seq tools v1.5. (Parameters: -e 50 -a -m 5000 --best --strata --nomaqround -y)
Genome_build: TAIR10
Supplementary_files_format_and_content: *.processed.txt: Tab-delimited text files include distinct sequences and reads count values.

value: polysomal ribosome profiling


title: Mono2 [sRNA]

description: Small RNA


title: Poly1 [sRNA]

description: Small RNA


title: Mono1 [RNA]


title: Mono1 [sRNA]

description: Small RNA


title: Poly2 [RNA]


title: RIP_anti_igg_6H_2

city: São Paulo

first: Lucas

middle: Ferreira

last: daSilva

state: São Paulo

address: Av. Vital Brasil 1500

department: Parasitology

country: Brazil

institute: Instituto Butantan

data_processing:
RIP-seq data from each of two independent biological replicates of each condition (2 anti-AR replicates and 2 control IgG replicates) were trimmed of low-quality reads and clipped of sequencing adaptors (Trimmomatic),
Aligned to hg19  version of the human genome  (TopHat 2) and assembled with Cufflinks 2.2
We used as reference for the alignment and assembly of the RIP-seq data a custom GTF file, which includes all expressed transcripts detected in the RNA-seq analysis of the LNCaP cells (see GSE79301) and lincRNAs from  GENCODE v19 (Harrow, Frankish et al. 2012) and those already annotated as lincRNAs in Cabili, Trapnell et al. 2011; Prensner, Iyer et al. 2011; Hangauer, Vaughn et al. 2013.
To detect the set of RNAs significantly associated with the AR, which we named AR-Associated lincRNAs (ARA-lincRNAs), we used the approach of (Soh, Mikedis et al. 2017), namely a DESeq2 analysis using HTSeq counting. A lincRNA was considered significantly associated with AR when the reads count ratio log2 (AR/IgG) > 0 and its FDR calculated with DEseq2 was below a threshold of 10 %.
Genome_build: hg19
Supplementary_files_format_and_content: RIP-Seq replicates analysed in DeSeq2 Tool (loci, strans, raito(ar/igg), adjusted p-value)

organism: Homo sapiens

source_name: Prostate

growth_protocol: LNCaP cells were obtained from the ATCC and grown as recommended in media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Gibco). Cells were cultured for 24 h in androgen-deprived RPMI 1640 (Sigma) with 10% (w/v) charcoal-stripped fetal bovine serum (Sigma) as described in (Louro, Nakaya et al. 2007).  After 24 h, cells were placed in fresh RPMI 1640 with 10% (w/v) charcoal-treated FBS and 0.1 nM of the synthetic androgen R1881 (Sigma)

extract_protocol:
The RNAs were extracted using Trizol, treated with TURBO DNase (Ambion) at 37 oC for 30 min, purified using an RNeasy Micro Kit (Qiagen) and quantified with RiboGreen (Invitrogen)
RNA samples from Native RIP were used to prepare sequencing libraries with the SMARTer Ultra Low Input RNA Kit for Sequencing v3 (Clontech) according to the manufacturer’s instructions, then sequenced on the Illumina NextSeq500 using 150 bp paired-end reads sequencing.

treatment_protocol: A native RIP was performed using the Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to the manufacturer's instructions with LNCaP cells treated for 6 h with 0.1 nM R1881 (Sigma) or vehicle (ethanol). The following antibodies were used from Millipore: Normal Rabbit IgG (12-370) and Anti-Androgen Receptor (06-680).

tag: cell line

value: LNCaP

tag: rip-antibody

value: Normal Rabbit IgG (Millipore 12-370)


title: TMU38(AA)_seedling-root_mRNA_rep2

description: mRNA


title: RIP_anti_AR_6H_2

value: Anti-Androgen Receptor (Millipore 06-680)


title: RIP_anti_AR_6H_1


title: RIP_anti_igg_6H_1


title: AT2(AADD)_endosperm_sRNA_rep3

description: small RNA

organism: Triticum urartu x Aegilops tauschii

tag: genotype

value: Synthetic allotetraploid wheat AADD


title: ER_ChIP-seq_MCF7_45min_E2+R5020

first: Hari

last: Singhal

address: 929 E 57th St

department: Ben May Department for Cancer Research

data_processing:
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using Bowtie2
The output from Bowtie2 (BAM files) was subjected to MACS14 to call ChIP-seq peaks. Corresponding inputs for each of the treatment conditions were used as the background.
If needed, the ChIP-seq peaks thus obtained were filtered based on false discovery rates and height of the peaks.
Vehicle treated ChIP-peaksets were subtracted from the hormone-treated ChIP-peaksets.
Genome_build: HG19
Supplementary_files_format_and_content: BED files

source_name: MCF7 cells

growth_protocol: Cells were cultured for 48 hours in charcoal-stripped serum media to deprive them of steroids.

extract_protocol:
Hormone-treated were harvested and ChIP was performed as per the directions provided in materials and method (ChIP and ChIP-sequencing)
ChIP-seq libraries were prepared using Kapa ChIP-seq kits. Details of library preparation strategy are provided in the materials and methods section (ChIP and ChIP-seq) of the paper.

treatment_protocol: Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM NR3C ligand (progesterone, dexamethasone, DHT or aldosterone) or 10 nM of both the hormones for 45 minutes or 4 hours.

tag: er/pr status

value: ER+/PR+

tag: drug treatment

tag: hormone exposure time

value: 45 minutes

tag: protocol

value: Cell models ChIP-seq

tag: chip antibody

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# L1911)


title: ER_ChIP-seq_MCF7_45min_E2

value: 10 nM E2


title: mir845 1n rep1

description: Small RNA

tag: ecotype

tag: tissue

value: Pollen


title: AT2(AADD)_endosperm_sRNA_rep1

description: small RNA

value: 6 days after pollination


title: ER_ChIP-seq_MCF7_45min_R5020


title: TRAP [sRNA]

description: Small RNA

data_processing:
Library strategy: TRAP
Basecalling pipeline: HiSeq Control Software 2.2.38; RTA 1.18.61.0; CASAVA-1.8.2.
FASTQ file generation and demultiplexing and adapter removal were done by Fasteris.
Small RNA reads were aligned to the Arabidopsis thaliana genome using the ncpro-seq tools v1.5. (Parameters: -e 50 -a -m 5000 --best --strata --nomaqround -y)
Genome_build: TAIR10
Supplementary_files_format_and_content: *.processed.txt: Tab-delimited text files include distinct sequences and reads count values.

tag: genotype/variation

value: overexpressing RPL18 fused in N terminal with a His6-Flag tag

value: TRAP


title: ER_ChIP-seq_MCF7_45min_Vehicle

value: Vehicle


title: AT2(AADD)_endosperm_mRNA_rep1

description: mRNA

tag: developmental stage


title: INPUT_MCF7

value: INPUT

value: 4 hours


title: ER_ChIP-seq_MCF7_4hrs_E2+Prog

value: 10 nM E2+10 nM Aldosterone


title: AT2(AADD)_endosperm_mRNA_rep3

description: mRNA


title: ER_ChIP-seq_MCF7_4hrs_E2+Aldo

value: 10 nM E2+10 nM DHT


title: Poly1 [RNA]

value: wild type

value: Inflorescences

value: polysomal ribosome profiling


title: ER_ChIP-seq_MCF7_4hrs_E2

value: ER+/PR+


title: ER_ChIP-seq_MCF7_4hrs_E2+DHT

value: 10 nM E2+10 nM Dexamethasone


title: ER_ChIP-seq_MCF7_4hrs_E2+Dex

value: 10 nM E2+10 nM Progesterone

value: Cell models ChIP-seq


title: AT2(AADD)_seedling-root_mRNA_rep3

description: mRNA

value: 3-leaf stage

value: Synthetic allotetraploid wheat AADD


title: ER_ChIP-seq_MCF7_4hrs_Vehicle

value: anti-ER (SC biotech HC-20, cat# SC-543, lot# L1911)


title: AT2(AADD)_seedling-root_mRNA_rep1

description: mRNA


title: AT2(AADD)_seedling-root_mRNA_rep2

description: mRNA


title: H11_IDX14_Aldo_rep1_and_rep2_RNAseq

data_processing:
VIPER pipeline at CFCE, DFCI was used to perform RNA-seq analyses. The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using STAR.
Relative expression of transcripts were calculated by subjecting STAR output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
Supplementary_files_format_and_content: Fold induction relative to vehicle treatments is presented.

extract_protocol:
Hormone-treated cells were homogenized and total RNA was extracted using Qiagen RNAeasy kit
PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit. Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper.

treatment_protocol: Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM NR3C ligand (progesterone (PR), dexamethasone (GR), DHT (AR) or aldosterone (MR)) or 10 nM of both the hormones for the above-mentioned time.

value: 10 nM Aldosterone

value: 24 hours

value: Cell models RNA-seq


title: H9_IDX12_DHT_rep1_and_rep2_RNAseq

value: 10 nM DHT


title: H17_IDX21_E2+DHT_rep1_and_rep2_RNAseq


title: H15_IDX19_E2+Dex_rep1_and_rep2_RNAseq


title: H7_IDX10_Dex_rep1_and_rep2_RNAseq

value: 10 nM Dexamethasone


title: H19_IDX23_E2+Aldo_rep1_and_rep2_RNAseq

value: 10 nM E2+10 nM Aldosterone


title: H5_IDX8_Prog_rep1_and_rep2_RNAseq

value: 10 nM Progesterone


title: H13_IDX16_E2+Prog_rep1_and_rep2_RNAseq


title: H3_IDX6_E2_rep1_and_rep2_RNAseq

value: 10 nM E2


title: H1_IDX4_Vehicle_rep1_and_rep2_RNAseq

value: Vehicle


title: T47D xenografts_RNA-seq_EC313+ICI

data_processing:
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using TopHat.
Relative expression of transcripts were calculated by subjecting TopHat output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
Supplementary_files_format_and_content: Matrix containing normalized readcounts from each of the samples has been provided

source_name: T47D Xenografts

growth_protocol: Xenografts: Nude mice harboring ER+/PR+ T47D xenografts were treated with various drug combinations for at least 3 weeks. Drugs were either admnistered in the form of intra-peritoneal injections or as 25 mg 90 day release drug pellets (Innovative Research of America).

extract_protocol:
Frozen xenograft tumors were finely grinded using cold hammer and a pestle. The pestle was placed over dry ice to maintain it at low temperatures. The ground tumor was suspended in ice-cold PBS and dounce homogenized and subsequently washed twice with ice-cold PBS.
The cell pellets obtained from and washed xenografts were processed similar to the pellets obtained from in-vitro experiments (RNA-seq protocol). Hormone-treated cells were homogenized and total RNA was extracted using Qiagen RNAeasy kit. PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit.
Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper.

treatment_protocol: PR agonists (progesterone, MPA and R5020), PR-agonistic antagonist EC313, PR antagonist CDB4453 and SERMs (tamoxifen, raloxifene, bazedoxifene and fulvestrant), mice were injected intra-peritoneal for three weeks with 10 mg/kg/day of the respective drugs. Five injections per week were administered.  Mice in the CDB4124 experiment arm (Vehicle, CDB4124, Tamoxifen or CDB4124+Tamoxifen) were administered using 25 mg drug pellets. At the end of the duration of the experiment, mice were sacrificed; tumors were excised, weighed, fixed and snap-frozen for later analyses. RNA-seq was performed on these harvested xenografts.  (Xenograft experiments).

tag: tissue type

value: T47D Xenografts

value: 3 weeks


title: T47D xenografts_RNA-seq_Tamoxifen-rep2

value: ER+/PR+

value: Tamoxifen


title: T47D xenografts_RNA-seq_4124+Tamoxifen


title: T47D xenografts_RNA-seq_EC313+BZA


title: T47D xenografts_RNA-seq_Tamoxifen-rep1


title: T47D xenografts_RNA-seq_MPA+Tamoxifen

value: MPA+Tamoxifen


title: T47D xenografts_RNA-seq_EC313+Raloxifene


title: T47D xenografts_RNA-seq_EC313


title: T47D xenografts_RNA-seq_EC313+Tamoxifen


title: T47D xenografts_RNA-seq_Progesterone

value: Progesterone


title: T47D xenografts_RNA-seq_MPA

value: MPA


title: T47D xenografts_RNA-seq_Vehicle-rep1


title: TQ27(DD)_endosperm_sRNA_rep2

description: small RNA

organism: Aegilops tauschii

value: 6 days after pollination


title: TQ27(DD)_endosperm_sRNA_rep3

description: small RNA


title: TQ27(DD)_endosperm_mRNA_rep1

description: mRNA


title: TQ27(DD)_endosperm_mRNA_rep2

description: mRNA


title: TQ27(DD)_endosperm_mRNA_rep3

description: mRNA


title: TQ27(DD)_seedling-root_mRNA_rep3

description: mRNA

value: 3-leaf stage


title: TQ27(DD)_endosperm_sRNA_rep1

description: small RNA


title: TQ27(DD)_seedling-root_mRNA_rep2

description: mRNA


title: TLTU(SlSlAA)_endosperm_sRNA_rep3

description: small RNA

organism: Aegilops longissima x Triticum urartu

value: Synthetic allotetraploid wheat SlSlAA


title: T47D xenografts_RNA-seq_CDB4124


title: T47D xenografts_RNA-seq_Control-rep2

value: Control


title: TQ27(DD)_seedling-root_mRNA_rep1

description: mRNA


title: T47D xenografts_RNA-seq_R5020


title: TLTU(SlSlAA)_endosperm_mRNA_rep3

description: mRNA


title: TLTU(SlSlAA)_endosperm_sRNA_rep1

description: small RNA


title: TLTU(SlSlAA)_endosperm_mRNA_rep2

description: mRNA


title: T47D xenografts_RNA-seq_R5020+Tamoxifen


title: T47D xenografts_RNA-seq_Progesterone+Tamoxifen

value: Progesterone+Tamoxifen


title: Sample99

description: liver tissue slices

data_processing:
Data were pre-processed using Fastqc and aligned to the genome using Tophat.
Genome mapped reads were counted using htseq-count.
Statistical analysis was done using edgeR.
Genome_build: gadMor1
Supplementary_files_format_and_content: read counts (text files)

organism: Gadus morhua

source_name: Liver

extract_protocol:
Total RNA from tissue explants were isolated using BioRad total RNA isolation kit.
RNAseq libraries were prepared using Illumina TruSeq total RNA library prep kit and sequencing was performed on Illumina HiSeq2000 platform at the Tufts University Core Facility.

treatment_protocol: Atlantic cod liver explants were exposed to either DMSO (0.01%) or two different organophosphate flame retardants (TCPP, EHDPP) for either 24 and 48 hours.

tag: chemical

value: Mixture

tag: concentration

value: High

tag: exposure time (hr)


title: Sample89

description: liver tissue slices

value: DMSO


title: Sample82

description: liver tissue slices

value: EHDPP


title: Sample83

description: liver tissue slices

value: TCPP

value: Low


title: Sample85

description: liver tissue slices


title: Sample78

description: liver tissue slices


title: Sample77

description: liver tissue slices


title: Sample71

description: liver tissue slices


title: Sample63

description: liver tissue slices


title: Sample58

description: liver tissue slices


title: Sample47

description: liver tissue slices


title: Sample51

description: liver tissue slices


title: TLTU(SlSlAA)_endosperm_sRNA_rep2

description: small RNA


title: Sample34

description: liver tissue slices


title: Sample33

description: liver tissue slices


title: Sample32

description: liver tissue slices


title: Sample72

description: liver tissue slices


title: Sample24

description: liver tissue slices


title: Sample27

description: liver tissue slices


title: Sample19

description: liver tissue slices


title: Sample30

description: liver tissue slices


title: Sample17

description: liver tissue slices


title: TLTU(SlSlAA)_endosperm_mRNA_rep1

description: mRNA


title: Sample139

description: liver tissue slices


title: Sample87

description: liver tissue slices


title: Sample122

description: liver tissue slices


title: Sample110

description: liver tissue slices


title: Sample115

description: liver tissue slices


title: Sample73

description: liver tissue slices


title: Sample01

description: liver tissue slices


title: TL05(SlSl)_endosperm_sRNA_rep3

description: small RNA

organism: Aegilops longissima


title: Sample48

description: liver tissue slices


title: TL05(SlSl)_endosperm_sRNA_rep2

description: small RNA


title: TL05(SlSl)_endosperm_mRNA_rep1

description: mRNA


title: TL05(SlSl)_endosperm_mRNA_rep3

description: mRNA


title: TL05(SlSl)_endosperm_mRNA_rep2

description: mRNA


title: Immature proglottids

city: Beijing

first: Yiru

address: Chaoqian

department: R&D

institute: Beijing Honor Tech Co Ltd

data_processing:
Basecalls performed using CASAVA version 1.4
Supplementary_files_format_and_content: sequences and counts

organism: Moniezia expansa

source_name: Immature proglottids

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
microRNA libraries were prepared for sequencing using standard Illumina protocols

value: proglottids


title: Gravid proglottids

source_name: Gravid proglottids


title: mature proglottids

source_name: mature proglottids


title: Scolex-neck proglottids

source_name: Scolex-neck proglottids


title: TAHV_D6

status: Public on Dec 30 2017

first: Yibin

last: Zhu

address: Biotechnology building

department: School of Medicine

institute: Tsinghua University

description: microinjected with 100 M.I.D.50 viruses

data_processing:
HCS 2.012 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Aedes Aegypti genome using SOAPaligner/SOAP2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).
NOIseq method coming from Sonia Tarazona et al., Genome Research, 2011., was applied to screen differentially expressed genes between two groups
Genome_build: Aaegl3.3
Supplementary_files_format_and_content: Excel files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample ...

organism: Aedes aegypti

source_name: Whole mosquito

growth_protocol: Aedes Aegypti was reared at 28℃ and 80% humidity.

extract_protocol:
Whole mosquito were dissected from mosquitoes, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 7 days old mosquitos were microinjected with 100 M.I.D. 50 virus, then infected after 1, 6 days.

tag: strain

value: Liverpool strain

value: Whole mosquito

tag: age

tag: treatment

value: microinjected with 100 M.I.D.50 viruses

tag: extracted timepoint

value: 6 day


title: dsGFP

description: microinjected with dsRNA

extract_protocol:
Midguts were dissected from mosquitoes, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 7 days old mosquitos were blood fed BSA or DENV2 NS1, then treated after 4, 8,18 hours.

value: 7 days

tag: innoculated

value: GFP dsRNA


title: SFV_D6

description: microinjected with 100 M.I.D.50 viruses


title: dsRNA1-GABAA-R1

description: microinjected with dsRNA

value: AaGABAA R1 dsRNAs


title: DENV_D6

description: microinjected with 100 M.I.D.50 viruses


title: SINV_D6

description: microinjected with 100 M.I.D.50 viruses


title: AT2(AADD)_endosperm_sRNA_rep2

description: small RNA

value: 6 days after pollination

tag: genotype

value: Synthetic allotetraploid wheat AADD


title: Mock_D1

description: microinjected with 100 M.I.D.50 viruses

value: 1 day


title: BATV_D6

description: microinjected with 100 M.I.D.50 viruses


title: E14_rep2_RNAseq

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

institute: Fudan University

data_processing:
Illumina Casava software used for basecalling.
We trimmed and mapped reads to the mouse mm10 reference assembly (GRCm38) by the Tophat2 software (Kim et al., 2013). We used default parameters expect that we reduced maximum insertion and deletion length to 2 bp, and kept only uniquely mapped, “no mixed” and “no discordant” reads.
We calculated FPKM for GENCODE M7 gene models using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each replicate.

growth_protocol: To maintain ESCs in ground state or naïve state, mouse ESC lines (E14TG2a) were cultured in 2i /LIF conditions as described (Ying et al., 2008).

extract_protocol:
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq3000 system (lllumina).

tag: cell line

tag: cell state

value: ground state

tag: culture condition

value: 2i /LIF conditions


title: E14_rep1_RNAseq


title: TL05(SlSl)_endosperm_sRNA_rep1

description: small RNA


title: dsRNA2-GABAA-R1

description: microinjected with dsRNA


title: DENV_D1

description: microinjected with 100 M.I.D.50 viruses


title: JEV_D6

description: microinjected with 100 M.I.D.50 viruses


title: Mock_D6

description: microinjected with 100 M.I.D.50 viruses


title: Sample11

first: Neelakanteswar

description: liver tissue slices


title: BATV_D1

description: microinjected with 100 M.I.D.50 viruses


title: TAHV_D1

description: microinjected with 100 M.I.D.50 viruses


title: SINV_D1

description: microinjected with 100 M.I.D.50 viruses


title: SFV_D1

description: microinjected with 100 M.I.D.50 viruses


title: JEV_D1

description: microinjected with 100 M.I.D.50 viruses


title: oz94

city: St lucia

first: Ruidong

last: Xiang

state: QLD

address: Level 5, QBP, 306 Carmody rd,

institute: CSIRO

data_processing:
qualities were checked and fastq files were sent by Ramaciotti Centre for Genomics
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ovis aries3.1 whole genome using bowtie2 and TopHat with defualt parameters
counts (exon based) were calculated by HTSeq and were normalised by EdgeR VOOM
Supplementary_files_format_and_content: tab-delimited text files include EdgeR VOOM normalised values for each sample

organism: Ovis aries

source_name: ventral rumen wall

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult

tag: sample

tag: block

tag: liveweight (kg)

tag: ch4 g/d

tag: dry matter intake g/d


title: oz95


title: oz97


title: oz92


title: oz89


title: oz93


title: oz9


title: oz85


title: oz79


title: oz73


title: oz43


title: oz40


title: oz59


title: oz61


title: oz42


title: AT2(AADD)_endosperm_mRNA_rep2

description: mRNA

source_name: endosperm

tag: developmental stage


title: oz70


title: oz249


title: oz29


title: oz31


title: oz238


title: oz35


title: oz244


title: oz235


title: oz39


title: oz218


title: oz224


title: oz214


title: oz207


title: oz197


title: oz196


title: oz192


title: oz190


title: oz200


title: oz206


title: oz187


title: oz184


title: oz183


title: oz179


title: oz171


title: oz175


title: oz241


title: oz165


title: oz18


title: oz170


title: oz169


title: oz155


title: oz134


title: oz141


title: oz132


title: oz143


title: oz127


title: oz120


title: oz151


title: oz109


title: oz125


title: oz118


title: oz1


title: oz107


title: oz108


title: H3 petals

city: Wuhan

first: wenqin

last: fu

state: Hubei

address: No.1,Shizishan Street

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using Illumina Casava1.7 software.
Raw data was saved as fastq files, and the high-quality clean reads were obtained after filtering the dirty reads with adaptors or two N and low quality reads.
Clean reads of each sample were mapped to the genome of Brassica rapa using Tophat, allowing no more than two mismatched bases.
Mapped reads were normalized using the DESeq Bioconductor package.
Gene expression levels were calculated as fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) using Cufflinks and Cuffdiff.
Genome_build: The genome of Brassica rapa
Supplementary_files_format_and_content: Microsoft Excel files include the expression of gene(FPKM) in each sample, the length of each gene, gene symbol, the description of gene and so on.

organism: Brassica napus

source_name: Petals

growth_protocol: Plants were grown in the greenhouse

extract_protocol:
The petals on half-open flowers were collected in liquid nitrogen from the four samples, respectively, and kept at -80°C. Total RNA was extracted by guanidine isothiocyanate method and then treated with RQ1 DNase (Promega) to remove DNA.
Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80°C until used for sequencing.

tag: tissue

value: Petals

value: half-open flowers

tag: phenotype

value: yellow flower


title: U937_rep2_p66Shc

city: Tianjin

first: Zhe

address: Heping District Qixiangtai Road No. 22

institute: Tianjin Medical University

data_processing:
Library strategy: 4C-seq
For 4C-seq data analysis, clean sequencing data were used and reads which contain the primers, DpnII and Csp6I sites were selected.
The primer sequence was trimmed from reads using cutadapt version 1.11 with default parameters, then the Csp6I site was trimmed from reads using cutadapt version 1.11 with parameters -a GTAC -e 0 -m 10.
Reads were mapped to Human hg19 whole genome using bowtie v1.1.2 with parameters -S -v 2 -k 1 -m 1 -I 0.
The bam files were loaded into r3Cseq version 1.22.0 of R to count reads number and to calculate per million mapped reads (RPM) of each fragment.
Data were uploaded to the IGV for visualization.
Genome_build: Human hg19
Supplementary_files_format_and_content: bedGraph files include RPM values for each samples.

source_name: human leukemic monocyte lymphoma cells

growth_protocol: HUVEC was grown in EGM-2 (Lonza) at 37 °C, 5% CO2; U937 was grown in RPMI (Gibco) supplemented with 10% FBS (Gold, PAA) at 37 °C, 5% CO2.

extract_protocol:
HUVEC or U937 cells (5*10^6) were cross-linked with formaldehyde and treated with lysis buffer, nuclei were digested with DpnII (NEB) and ligated with T4 DNA ligase (NEB). Protein K was used for de-cross-link, and phenol-chloroform was used for the genomic DNA extraction. Subsequently, the extracted genomic DNA was digested with Csp6I (NEB) in a second round, and the DNA was ligated again with T4 DNA ligase (NEB).
Specific primers were designed near the p66Shc promoter. The viewpoint was a 562bp DNA fragment which coordinated at -335bp ~+227bp of p66Shc TSS. Illumina adaptors were included in the primers. PCRs were performed with Expand Long Template PCR System (Roche), PCR products were purified using QIAquick PCR Purification Kit (Qiagen) and the sample concentrations were measured by Qubit dsDNA BR Assay Kit (Thermo Fisher). All samples were sequenced using PE150 program with Illumina Hi-Seq X Ten.

treatment_protocol: 4C target enrichment

value: Wild type

tag: enzyme


title: U937_rep1_p66Shc


title: HUVEC_rep1_p66Shc

source_name: primary human umbilical vessel endothelial cells

value: HUVEC


title: oz10

tag: age


title: oz166


title: oz152


title: ISX-9 - Sample 4 (miRNA)

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

data_processing:
Basecalls performed using Illumina Basespace
miRNA-seq reads were aligned to the miRBase 21 assembly using BWA mem version 0.7.5
The raw count of short reads were quantified using featureCounts version 1.5.0
Genome_build: miRBase 21
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample. Each row corresponds to one miRNA. Each column correspond to one sample.

source_name: cardiac progenitors from ATCC-CYS0105 Human Induced Pluripotent Stem Cell

growth_protocol: The Human iPSC cell line (ACS-1021™) was purchased from ATCC Company.Undifferentiated hiPSCs were maintianed on vitronectied coated plates in meTSR1 medium. For differentiation,briefly, iPSCs maintained on vitronectin coated six-well plate in mTeSR1 were dissociated into single cells using accutase (Invitrogen) at 37℃ for 10 min and then were seeded on to a vitronectin-coated six-well plate at 1×10e6 cell/well in mTeSR1 supplemented with 5μM ROCK inhibitor(Y-27632, stem cell technology) for 24 h. Afterwards cells were cultured in mTesR1, which was changed daily. After 3 days, the medium was switched to RPMI/B27 minus insulin supplemented with ISX-9 (20uM, dissolved in DMSO) or for 7 days.

extract_protocol:
Total RNA containing miRNA was extracted from cells using Qiagen’s RNasey Plus Mini kit according to manufacturer’s instructions followed by DNAse treatment using RNase-free DNase kit (Qiagen).
Sequencing libraries were prepared using Illumina’s TruSeq Small RNA Core solutions kit + Truseq Small RNA Indices A kit(Illumina product #s respectively: 15016911 and 15016912). Input amount for library preparation was 1 ug of total RNA per sample. Libraries were PCR amplified at 11 cycles and quantified using Qubit dsDNA HS assay. Sequencing libraries were pooled in equimolar concentrations and sequencing was performed on NextSeq 500 (Illumina), single read 75 nt, high output (about 400 million reads per lane).

treatment_protocol: Three treatment groups: undiffentiated hiPSC in mTeSR1; monolayer hiPSCs treated with ISX-9 (20uM, dissolved in DMSO); monolayer hiPSCs treated with DMSO(0.5%)

tag: cell type

value: Monolayer cardiac fibroblast-derived hiPSC

tag: treatment

tag: growth protocol

value: in RPMI/B27 minus insulin for 7 day

tag: cell status

value: differentiated cells


title: M4 petals

value: red flower


title: DMSO - Sample 1 (miRNA)

source_name: ATCC-CYS0105 Human Induced Pluripotent Stem Cell treated with DMSO

value: DMSO


title: hiPSC - Sample 4 (miRNA)

source_name: ATCC-CYS0105 Human Induced Pluripotent Stem Cell

value: undifferentiated hiPSCs, derived from cardiac fibroblast

value: in meTSR1 medium

value: undifferentiated hiPSC


title: ISX-9 - Sample 1 (miRNA)


title: DMSO - Sample 3 (miRNA)


title: ISX-9 - Sample 2 (miRNA)


title: HUVEC_rep2_p66Shc

tag: cell line

tag: genotype


title: DMSO - Sample 2 (miRNA)


title: ISX-9 - Sample 3 (miRNA)


title: hiPSC - Sample 3 (miRNA)


title: hiPSC - Sample 2 (miRNA)


title: hiPSC - Sample 1 (miRNA)


title: DMSO - Sample 3 (mRNA)

data_processing:
Basecalls performed using Illumina Basespace
3' RNA-seq reads were aligned to the UCSC hg19 genome assembly using BWA mem version 0.7.5
The raw count of short reads were quantified using featureCounts version 1.5.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample . Each row corresponds to one gene. Each column corresponds to one sample.

extract_protocol:
Total RNA containing miRNA was extracted from cells using Qiagen’s RNasey Plus Mini kit according to manufacturer’s instructions followed by DNAse treatment using RNase-free DNase kit (Qiagen).
Sequencing libraries were prepared using QuantSeq 3’mRNA-Seq Library Kit (Lexogen Inc, product # 015.96). Input amount for the library preparation was 500 ng of total RNA per sample. Libraries were PCR amplified at 16 cycles and quantified using Qubit dsDNA HS assay. Sequencing libraries were pooled in equimolar concentrations and sequencing was performed on NextSeq 500 (Illumina), single read 75 nt, high output (about 400 million reads per lane).
3’mRNA-seq


title: ISX-9 - Sample 3 (mRNA)


title: DMSO - Sample 4 (mRNA)


title: DMSO - Sample 1 (mRNA)


title: DMSO - Sample 2 (mRNA)


title: ISX-9 - Sample 4 (mRNA)


title: hiPSC - Sample 4 (mRNA)


title: DMSO - Sample 4 (miRNA)


title: hiPSC - Sample 1 (mRNA)


title: ISX-9 - Sample 2 (mRNA)


title: Mac Trpc3 knocout-3

city: Toledo

first: Guillermo

last: Vazquez

state: OH

address: 3000 Arlington Ave

department: Physiology and Pharmacology

institute: University of Toledo College of Medicine and Life Sciences

data_processing:
Illumina Casava software used for basecalling.
To prepare the reads for alignment, the sequencing adapters and other low quality bases were clipped(1).  Reads were aligned to External RNA Controls Consortium (ERCC) sequences to assess the success of library construction and sequencing.
A subset of the reads (~1 million reads) were aligned to other spiked-in control sequences (PhiX and other Illumina controls used during library preparation), residual sequences (globin and ribosomal RNA), and poly-A/T sequences that persisted after clipping.  The reads were also aligned to a sampling of intergenic regions to assess the level of DNA contamination level.
To quantify transcripts, RSEM v1.2.0 was used to quantify genes and transcripts (2) using the UCSC knownGene transcriptome.  Reads that remained unaligned to the transcriptome may be due to miss annotation, lack of annotation, or from genomic DNA.  To determine the origin of all reads as a method of quality control, the unaligned reads were aligned to the full genome (not transcriptome) using BWA 0.6.23 (3).          References   1.  Erik Aronesty (2013). TOBioiJ : "Comparison of Sequencing Utility Programs", 2. Li and Dewey BMC Bioinformatics 2011, 12:323.  3.  Li and Durbin Bioinformatics 2009 [PMID: 19451168].
Genome_build: mm10

source_name: MacTrpc3-deficient -KO-3

extract_protocol:
Bone marrow-derived macrophages, in vitro differentiation to the M1 type and Total RNA was extracted using 5 PRIME PerfectPure™ Purification System (5prime). TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2103) was used with 100ng of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Bone marrow derived Macrophages

tag: gender

value: Male

value: 8 Weeks


title: Mac Trpc3 knocout-1

source_name: MacTrpc3-deficient -KO-1


title: Trpc3lox/lox-3


title: DKO_NP WGBS

city: Seoul

first: Jungwoo

last: Lee

address: 50 Yonsei-ro Seodaemun-gu

country: South Korea

institute: Yonsei University

data_processing:
The Illumina HiSeq X Ten (Illumina, San Diego, CA, USA) generates raw images and base calling was done through BS-mapping tool called bismark (Babraham Bioinformatics). Bisulfite conversion efficiency was > 98.5% in all samples. And a CpG coverage threshold of ≥10 was used.
Genome_build: mm9

source_name: Neural progenitor cells

growth_protocol: Wild-type (background-J1) and Dnmt3a/b DKO ESCs were cultured under standard conditions [KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol and leukemia inhibitory factor (LIF)]. For earlier passages, cells were maintained on an irradiated feeder layer, which was later removed by passaging cells for at least two passages off of the feeder cells onto gelatin-coated plates. ESCs were differentiated into the NPC through embryoid body formation for 4 days, followed by treatment with 5M retinoic acid for additional 2 days.

extract_protocol: Genomic DNA was extracted from J1 and Dnmt3 double KO ESCs using the Qiagen Centra Puregene kit. 300ng of genomic DNA was treated with bisulfite and followed by random primed DNA synthesis. All procedures were performed according to the manufacturer’s instructions (TruSeq DNA Methylation kit, Illumina, San Diego, CA, USA).

value: ES-derived neural progenitor cells

tag: passages

value: day 6


title: Trpc3lox/lox-1


title: OvW petals

organism: Orychophragmus violaceus

value: Petals

value: half-open flowers

value: white flower


title: DKO_ES WGBS

organism: Mus musculus

source_name: Embryonic stem cells

value: Embryonic stem cells

value: day 0


title: WT_NP WGBS


title: Trpc3lox/lox-2


title: WT_ES

data_processing:
Reads for mRNA-seq were mapped to the mouse genome mm9 using Bowtie and Tophat allowing one mismatch and tracking up to 50 best alignments per read and default parameter values.
Genome_build: mm9

extract_protocol:
Total RNA was extracted from J1 and Dnmt3 double KO ESCs. 5 μg of RNA was subjected to rRNA depletion, fragmentation, and cDNA synthesis following the TruSeq RNA Sample Preparation guide (Illumina).
End repair, addition of a single dA, ligation with indexed adaptors, and 15 cycles of PCR with Illumina primers were performed also following the TruSeq RNA Sample Preparation guide. RNA-seq library was purified using AMPure XP beads (Agencort) and quantified its size distribution on a TapeStation Instrument (Agilent Technologies). Single-end sequencing was performed on Illumina HiSeq 2000 with 50 cycles.

tag: genotype/variation

value: wild type


title: WT_NP


title: ISX-9 - Sample 1 (mRNA)

value: Monolayer cardiac fibroblast-derived hiPSC

value: in RPMI/B27 minus insulin for 7 day

value: differentiated cells


title: WT_ES WGBS


title: MM6 input

status: Public on Dec 29 2017

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m6A-seq reads were aligned to the GRCh38 genome assembly using Tophat 2.1.1
peaks were called using exomePeak
the m6A peaks were annotated using an ad hoc perl script.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated by MACS2 and bedGraphToBigWig. BedWig files can be uploaded to UCSC Genome Browser for visualization

source_name: MM6 cell

extract_protocol:
RNA was extracted by Trizol. Polyadenylated RNA was purified using Dynabeads mRNA DIRECT kit (ThermoFisher)
RNA fragmentation, m6A-Seq and library preparation were performed according to previous protocols (Dominissini et al., 2012)

value: MonoMac 6

value: acute monocytic leukemia cell

tag: shRNA

value: shNS (non-specific control)

tag: antibody

value: none (input)


title: NB4-shNS IP

source_name: NB4 cell

tag: antibody vendor

value: Synaptic Systems

tag: antibody cat. #


title: MM6-shM14-#2 IP


title: NB4-shM14-#1 IP


title: hiPSC - Sample 3 (mRNA)

value: undifferentiated hiPSCs, derived from cardiac fibroblast

value: in meTSR1 medium

value: undifferentiated hiPSC


title: DKO_ES

value: DNMT3A/B DKO


title: MM6-shM14-#1 IP


title: DKO_NP

value: ES-derived neural progenitor cells

value: day 6


title: NB4-shM14-#2 IP


title: hiPSC - Sample 2 (mRNA)


title: MM6-shNS IP


title: NB4 input


title: Mac Trpc3 knocout-2

source_name: MacTrpc3-deficient -KO-2

tag: tissue

value: Bone marrow derived Macrophages

value: Male

value: 8 Weeks


title: YFFY_totalRNA_scriptSeq_rep1

city: Macclesfield

first: Muhammad

middle: Ahmad

last: Maqbool

address: Alderley Park

department: Cancer Research UK Manchester Institut

institute: University of Manchester

description: Total RNA-seq from cells expressing HA tagged mutant RNA Polymerase II. Libraries were prepared using ScriptSeq V2 total RNA kit from Epicenter.

data_processing:
All sequencing reads were aligned to the hg19 genome assembly using Bowtie2 or TopHat2 (allowing 2 mismatches, keeping uniquely aligned reads only).
For ChIP-seq experiments, all samples were input subtracted and signals were scaled so that the same number of units appeared in each experiment after merging of the replicates.
For RNA-seq experiments, reads that aligned to + or – strand were seperated and processed seperately to produce WIG files with strand specific enrichment scores.
Genome_build: hg19

source_name: Raji B cells

growth_protocol: Human Raji B cells were cultured under standard growth conditions and transfected with full-length recombinant Rpb1 expression plasmids (rWT, YFFF, YYFF, FYYF, YFFY and S2AAA). Polyclonal cell lines were established after G418 (1 mg/mL) selection for 2-3 weeks. Expression of mutant Rpb1 was induced by culturing the cells in Tetracycline free medium. 24 hours after induction, 2 µg/mL α-amanitin was added to inhibit endogenous Rpb1.

extract_protocol:
Cells were harvested at 72 hours after induction (48 hours after α-amanitin) to perform ChIP using specific antibodies or total RNA, polyA-RNA and Nascent RNA was extracted using corresponding protocols as described in manuscript.
ChIP-seq libraries were prepared with Illumina's ChIP Sample Prep Kit according to standard protocol. RNA-seq Libraries were prepared either with Illumina's Small RNA Library Prep Kit by using a modified protocol described in manuscript or with Epicenter's ScriptSeq V2 library preparation protocol according to manufacturer's instructions.

value: YFFY


title: YYFF_totalRNA_scriptSeq_rep2

value: YYFF


title: OvP petals

value: Petals

tag: developmental stage

value: half-open flowers

tag: phenotype

value: purple flower


title: YFFY_totalRNA_scriptSeq_rep2


title: YYFF_totalRNA_scriptSeq_rep1


title: YFFF_totalRNA_scriptSeq_rep2

value: YFFF


title: FYYF_totalRNA_scriptSeq_rep1

value: FYYF


title: FYYF_totalRNA_scriptSeq_rep2


title: rWT_totalRNA_scriptSeq_rep2

description: Total RNA-seq from cells expressing HA tagged WT RNA Polymerase II. Libraries were prepared using ScriptSeq V2 total RNA kit from Epicenter.

value: rWT


title: rWT_totalRNA_scriptSeq_rep1


title: YFFF MNase-seq replicate2

description: MNase digested nucleosomal DNA sequencing from cells expressing HA tagged mutant RNA Polymerase II


title: YFFF MNase-seq replicate1


title: rWT MNase-seq replicate2

description: MNase digested nucleosomal DNA sequencing from cells expressing HA tagged WT RNA Polymerase II


title: YFFF chrRNA replicate2

description:
chromatin associated RNA
Chromatin tethered RNA-seq from cells expressing HA tagged mutant RNA Polymerase II


title: YFFF polyARNA replicate1

description: Polyadenylated RNA-seq from cells expressing HA tagged mutant RNA Polymerase II


title: rWT polyARNA replicate1

description: Polyadenylated RNA-seq from cells expressing HA tagged WT RNA Polymerase II


title: rWT polyARNA replicate2


title: rWT MNase-seq replicate1


title: rWT chrRNA replicate1

description:
chromatin associated RNA
Chromatin tethered RNA-seq from cells expressing HA tagged WT RNA Polymerase II


title: rWT chrRNA replicate2


title: YFFF totalRNA replicate2

description: Total RNA-seq from cells expressing HA tagged mutant RNA Polymerase II


title: YFFF polyARNA replicate2


title: rWT H3K27ac ChIP replicate1

description: H3K27ac ChIP from cells expressing HA tagged WT RNA Polymerase II

tag: chip antibody


title: rWT H3K27ac ChIP replicate2


title: rWT totalRNA replicate2

description: Total RNA-seq from cells expressing HA tagged WT RNA Polymerase II


title: YFFF_totalRNA_scriptSeq_rep1


title: rWT H3K4me3 ChIP replicate1

description: H3K4me3 ChIP from cells expressing HA tagged WT RNA Polymerase II


title: YFFF H3K4me1 ChIP replicate1

description: H3K4me1 ChIP from cells expressing HA tagged mutant RNA Polymerase II


title: YFFF H3K4me3 ChIP replicate2

description: H3K4me3 ChIP from cells expressing HA tagged mutant RNA Polymerase II


title: YFFF H3K4me3 ChIP replicate1


title: rWT totalRNA replicate1


title: rWT H3K4me1 ChIP replicate2

description: H3K4me1 ChIP from cells expressing HA tagged WT RNA Polymerase II


title: YFFF PolII ChIP replicate1

description: Pol II ChIP from cells expressing HA tagged mutant RNA Polymerase II


title: YFFF totalRNA replicate1


title: rWT H3K4me1 ChIP replicate1


title: rWT H3K4me3 ChIP replicate2


title: rWT PolII ChIP replicate2

description: Pol II ChIP from cells expressing HA tagged WT RNA Polymerase II


title: YFFF H3K27ac ChIP replicate2

description: H3K27ac ChIP from cells expressing HA tagged mutant RNA Polymerase II


title: rWT PolII ChIP replicate1


title: YFFF chrRNA replicate1


title: YFFF PolII ChIP replicate2


title: YFFF H3K27ac ChIP replicate1


title: M81 CHX treated 01

city: Heidelberg

first: Henri-Jacques

last: Delecluse

address: Im Neuenheimer Feld 280

department: Pathogenesis of Virus Associated Tumors

institute: DKFZ

description:
Sample 9
ribosome-protected RNA fragments
ribosome footprints from cells infected with the M81 EBV strain, pretreated with cycloheximide
uORFs.tsv
comparison-human-cycloheximide.tsv
M81 libraries.txt

data_processing:
Library strategy: ribosome profiling
Basecalls were performed using RTA 1.17.21.3
Linker sequences were removed using fastx_clipper.
Alignments were performed using STAR. Reads aligning to rRNA sequences were discarded and the remaining ribosome footprints were aligned to the human genome (issue HG-19) and the EBV genomes B95-8 (accession # NC_007605) and M81 (accession # KF373730.1).
Genome_build: hg19 (GRCh37); NC_007605.1; KF373730.1
Supplementary_files_format_and_content: ribosome footprints

source_name: B cells

growth_protocol: EBV-transformed B cells and HEK293 cells were maintained in RPMI-1640 medium (Invitrogen). B cells were subpassaged every 3-4 days, depending on cell density. HEK293 cells were routinely split at a 1:7 ratio by resuspension and transfer onto a new culture dish.

extract_protocol:
Lysates were clarified by centrifugation and ribosome covered RNA was isolated by sucrose gradient ultracentrifugation and subsequent fractionation. Isolated fractions were RNAse I treated for 15 minutes at room temperature. Following nuclease treatment ribosome protected fragments were gel purified.
Libraries for highthroughput sequencing were generated according to the published protocol from Ingolia et al. 2012 published in Nature Protocols.

treatment_protocol: Cycloheximide treatment was performed at 37°C for 10 minutes at a concentration of 100µg/ml. Harringtonine treatments were performed at 37°C for 2 or 5 minutes at a concentration of 2µg/ml.

tag: cell type

value: CD19+ B cells

tag: in vitro transformed by

value: EBV strain M81

tag: treatment

value: pretreated with cycloheximide


title: M81 2 min Harr treated 01

description:
Sample 6
ribosome-protected RNA fragments
ribosome footprints from cells infected with the M81 EBV strain, pretreated for 2 minutes with harringtonine
uORFs.tsv
comparison-harringtonine.tsv
M81 libraries.txt


title: M81 2 min Harr treated 02

description:
Sample 8
ribosome-protected RNA fragments
ribosome footprints from cells infected with the M81 EBV strain, pretreated for 2 minutes with harringtonine
uORFs.tsv
comparison-harringtonine.tsv
M81 libraries.txt


title: M81 5 min Harr treated 01

description:
Sample 7
ribosome-protected RNA fragments
ribosome footprints from cells infected with the M81 EBV strain, pretreated for 5 minutes with harringtonine
uORFs.tsv
comparison-harringtonine.tsv
M81 libraries.txt


title: 293-2089 2 min Harr treated 01

description:
Sample 10
ribosome-protected RNA fragments
ribosome footprints from HEK293 cells stably transfected with the B95-8 BACMID and induced into lytic replication, pretreated for 2 minutes with harringtonine
uORFs.tsv
293-2089 library.txt

source_name: human embryonic kidney cells

value: HEK293 cells

value: EBV strain B95-8


title: H3K27me2me3_input_N5865_AR16_FGSC2643_ACTTGA_121514

city: Eugene

first: Eric

last: Selker

state: Oregon

address: 1370 Franklin Blvd.

department: Biology

institute: University of Oregon

data_processing:
For Poly-A mRNA seq: high quality, adapter-less reads were identified (Stacks); Kmer filtering reduced sequencing errors. Reads were mapped (TopHat) to the modified Neurospora genome assembly 12, and sorted (SAMTools), and directionality-preserved read numbers were calculated at each gene ID (HTSeq), adding one read count to prevent abnormal fold changes. Differential gene expression analysis (DESeq) examined replicate differences and pair-wise analyses between WT and translocations.
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al., 2011, Nat. Biotechnol.), reads were mapped with bowtie2 to the nc12-fixed genome (Galazka et al., 2016) using default parameters, and reads were converted to .bam files, sorted, and indexed. The .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 200bp windows. Output file was a .tdf file, displayable on IGV.
For whole-genome-seq breakpoint analysis: Incongruous-paired and split-read alignments for input DNA samples were found using bwa-mem. The discordant and split-read alignments were analyzed with LUMPY v0.2.9 to determine the location of chromosomal breakpoints (Layer et al. 2014). A list of predicted breakpoints with a minimum call weight of five was generated and calls with an evidence set score <0.05.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024).
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 25 -200bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV). The bcf files were produced from bam files (mapped to the Neurospora crassa assembly 12 Fixed by samtools), and report enrichment values.
Supplementary_files_format_and_content: For Poly-A mRNA files: Text files contain counts for every gene as outlined in process above.
Supplementary_files_format_and_content: For whole-genome-seq: bedpe files contain list of predicted breakpoints predicted by LUMPY.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.

extract_protocol:
RNA-seq: Mycelia were harvested and added to a tube containing ~350uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at room temperature. Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH. Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNase (DNA-free™ DNA Removal Kit, Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
ChIP-seq: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP. Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% Triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 2uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit and eluted in 30 μl of water.
Whole-genome-seq: Used input DNA from ChIP experiments.
RNA-seq: RNA-seq libraries were prepared (KAPA Stranded mRNA-seq kit, KAPA Biosystems).
ChIP-seq: Approximately 10 ng of DNA was used to generate ChIP-Seq libraries. Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions. “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606). Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.
Whole-genome-seq: Performed library prep same as ChIP-seq samples.

value: germinated conidia


title: B95-8 2 min Harr treated 02

description:
Sample 3
ribosome-protected RNA fragments
ribosome footprints from cells infected with the B95-8 EBV strain, pretreated for 2 minutes with harringtonine
uORFs.tsv
comparison-harringtonine.tsv
B95-8 libraries.txt


title: H3K27me2me3_input_N5863_OY320_FGSC3635_GATCAG_121514


title: B95-8 CHX treated 01

description:
Sample 4
ribosome-protected RNA fragments
ribosome footprints from cells infected with the B95-8 EBV strain, pretreated with cycloheximide
uORFs.tsv
comparison-human-cycloheximide.tsv
B95-8 libraries.txt


title: B95-8 5 min Harr treated 01

description:
Sample 2
ribosome-protected RNA fragments
ribosome footprints from cells infected with the B95-8 EBV strain, pretreated for 5 minutes with harringtonine
uORFs.tsv
comparison-harringtonine.tsv
B95-8 libraries.txt


title: H3K27me2me3_input_N5859_UK2-32_FGSC7294_ACAGTG_121514


title: H3K27me2me3_input_N5862_OY350_FGSC4641_TAGCTT_121514


title: H3K27me2me3_input_N5101_ALS159__FGSC2100_CAGATC_121514


title: H3K27me2me3_input_N5100_AR16_FGSC1614_ATCACG_121514


title: H3K27me2me3_input_N5102_OY329_FGSC3670_CGATGT_121514


title: H3K27me2me3_input_N6228_tert_GTGCCA_063016


title: H3K27me2me3_N5865_AR16_FGSC2643_GTTTCG_121514

value: H3K27me2me3 (ActiveMotif; cat# 39535)


title: H3K27me2me3_N5857_NM149_FGSC1483_CCGTCC_121514


title: H3K27me2me3_N5862_OY350_FGSC4641_CGTACG_121514


title: H3K27me2me3_N5859_UK2-32_FGSC7294_GTCCGC_121514


title: H3K27me2me3_N5858_OY337_FGSC3668_GAGTGG_121514


title: H3K27me2me3_N5866_UK3-41_FGSC6869_ATTCCT_121514


title: H3K27me2me3_N6383_csr-1_tel-repeats_GTAGCA_063016


title: H3K27me2me3_N6228_tert_TAGGAA_012716


title: H3K27me2me3_N5863_OY320_FGSC3635_CCGTCC_012915


title: H3K27me2me3_N6089_OY329dup_GCCAATAT_081415


title: H3K27me2me3_input_N5866_UK3-41_FGSC6869_AGTTCC_121514


title: B95-8 2 min Harr treated 01

description:
Sample 1
ribosome-protected RNA fragments
ribosome footprints from cells infected with the B95-8 EBV strain, pretreated for 2 minutes with harringtonine
uORFs.tsv
comparison-harringtonine.tsv
B95-8 libraries.txt


title: N5866_UK3-41_FGSC6869_polyA-mRNA


title: H3K27me2me3_N51_MV_FGSC2225_GTGAAA_022515


title: N6086_N6087_N5102_delta set-7_polyA-mRNA


title: N5862_OY350_FGSC4641_polyA-mRNA


title: N5859_UK2-32_FGSC7294_polyA-mRNA


title: N5858_OY337_FGSC3668_polyA-mRNA


title: M81-transformed LCLs sample 2

description:
RNA-Seq M81 sample 2
Processed data file: Human genes_RPKM.tsv
Processed data file: M81 viral genes_RPKM.txt
Processed data file: M81_new viral genes_RPKM.txt

data_processing:
Sequenced reads were trimmed for adaptor sequences and mapped to the HG-19 human genome using star.
Unmapped sequences were then further mapped to the viral genomes of B95-8 (NC_007605.1) and M81 (KF373730.1) using tophat2.
The remaining unmapped sequences were then mapped to the new EBV genes identified by O'Grady et al.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to Mortazavi et al. Nature Methods 2008.
Genome_build: hg19 (GRCh37); NC_007605.1; KF373730.1
Supplementary_files_format_and_content: *_libraries_RPF.txt: Tab-delimited text files contain normalized ribosome coverage for each Sample.
Supplementary_files_format_and_content: *_RPKM.txt: Tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Lysates were clarified by centrifugation and ribosome covered RNA was isolated by sucrose gradient ultracentrifugation and subsequent fractionation. Isolated fractions were RNase I treated for 15 minutes at room temperature. Following nuclease treatment, ribosome protected fragments were gel purified. For total RNA sequencing, cells were lysed with Trizol (Ambion) reagent and RNA was purified according to manufacturer's instructions.
Ribosome profiling libraries for high-throughput sequencing were generated according to the published protocol from Ingolia et al. 2012 published in Nature Protocols. The total RNA sequencing libaries were prepared by the DKFZ core facility using the strand-specific RNA preparation kit from Agilent.

treatment_protocol: Cycloheximide treatment was performed at 37°C for 10 minutes at a concentration of 100µg/ml. Harringtonine treatments were performed at 37°C for 2 or 5 minutes at a concentration of 2µg/ml. For total RNA sequencing, the samples were left untreated.


title: MM6-shM14-#2-rep2 [RNA-Seq]

description:
processed data file:
KnockDown2_vs_Control2.all.gene.result.xls
JC-HW20_GTGAAA

data_processing:
sequence reads were aligned to the genome by using standard Illumina sequence analysis pipeline
Genome_build: GRCh19
Supplementary_files_format_and_content: the expression and p value

extract_protocol:
RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, CA). NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
Library was prepared by or NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).

tag: cell line

value: MonoMac 6

tag: tumor

value: acute monocytic leukemia


title: N5102_OY329_FGSC3670_polyA-mRNA


title: MM6-shNS-rep2 [RNA-Seq]

description:
processed data file:
KnockDown2_vs_Control2.all.gene.result.xls
JC-HW19_ACAGTG

value: shNS (non-specific control)


title: N5100_AR16_FGSC1614_polyA-mRNA


title: N5101_ALS159_FGSC2100_polyA-mRNA


title: MM6-shM14-#2-rep1 [RNA-Seq]

description:
processed data file:
KnockDown2_vs_Control2.all.gene.result.xls
JC-HW18_ATTCCT


title: MM6-shNS-rep1 [RNA-Seq]

description:
processed data file:
KnockDown2_vs_Control2.all.gene.result.xls
JC-HW17_ACTGAT


title: B95-8-transformed LCLs sample 2

description:
RNA-Seq B95-8 sample 2
Processed data file: Human genes_RPKM.tsv
Processed data file: B95-8 viral genes_RPKM.txt
Processed data file: B95-8_new viral genes_RPKM.txt


title: H3K27me2me3_N5101_ALS159_FGSC2100_GTGGCC_121514


title: B95-8-transformed LCLs sample 1

description:
RNA-Seq B95-8 sample 1
Processed data file: Human genes_RPKM.tsv
Processed data file: B95-8 viral genes_RPKM.txt
Processed data file: B95-8_new viral genes_RPKM.txt


title: NB4-shM14-#2-rep2 [RNA-Seq]

description:
processed data file:
KnockDown1_vs_Control1.all.gene.result.xls
JC-HW16_GTGGCC


title: NB4-shNS-rep1 [RNA-Seq]

description:
processed data file:
KnockDown1_vs_Control1.all.gene.result.xls
JC-HW13_GCCAAT


title: NB4-shM14-#2-rep1 [RNA-Seq]

description:
processed data file:
KnockDown1_vs_Control1.all.gene.result.xls
JC-HW14_ACAGTG