title: JIA patient 15_clinical_remission

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_4


title: Fuji  125mg/kg Tazemetosta 7 day treatment BID 7Fuji-10_L5.D704

status: Public on Jun 18 2016

type: SRA

city: Cambridge

first: Igor

last: Feldman

address: 400 Technology Square

country: USA

institute: Epizyme

library_source: transcriptomic

data_processing: The raw read counts were transformed using voom and quantile normalized, which results in expression measures (summarized intensities) in log base 2.  Statistical analysis was subsequently performed using empirical Bayes from the limma R package.  Normalized data provide the input for statistical hypothesis testing, in which genes are identified that are statistically significantly different between sample groups, i.e. differences that are unlikely to be due to chance.  The degree of difference, i.e. the fold-change, is also accounted for.  In the output, the fold-changes (logFC) are given as log2 values, with a positive logFC representing up-regulation, and a negative logFC indicating down-regulation.  For each comparison (e.g. A-B, which is the same as 'A relative to B'), the first group (A) is the numerator, while the second group (B) is the denominator.  Thus, a positive logFC for the comparison 'A-B' indicates up-regulation in A relative to B.  Comparisons were undertaken using linear modelling.  Subsequently, empirical Bayesian analysis was applied (including vertical p-value adjustment for multiple testing, which controls for false discovery rate).  For each comparison, the null hypothesis was that there was no difference between the groups being compared.  Significant genes with adjusted P<0.05 from each comparison were analyzed for enrichment of KEGG and GO pathway membership using a hypergeometric test.  Enrichment (P<0.05) was assessed for up- and down-regulated genes separately.  The results from the three separate xenograft models were taken and a congruence analysis was performed to determine the extent of overlap between the differentially expressed genes and significantly enriched KEGG pathways and GO terms between cell lines.

molecule: total RNA

organism: Homo sapiens

source_name: Fuji Xenograft model

growth_protocol: All the procedures related to animal handling, care, and the treatment in this study were performed according to the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) of Champions Oncology and Eisai Tsukuba following the guidance of the Association for Assessment and Accreditation of Laboratory Animal Care. HS-SY-II xenograft studies were performed at Eisai Tsukuba (pharmacodynamics study) and HAMRI Tsukuba Research center (efficacy study).  The protocols were approved by the IACUC of Eisai Tsukuba (Permit Number: 13-D-0307-001 for efficacy study and 13-D-0154-001 for pharmacodynamics study).  HS-SY-II cells were harvested during mid-log phase growth, and resuspended in PBS with 50% Matrigel (BD Biosciences).  Balb/C-nu mice (Charles River Laboratories Japan) received 1 × 107 cells (0.1 mL cell suspension) subcutaneously in the right flank.  Mice carrying tumors of approximately 170 mm3 for efficacy study (35 days after injection) or 220 mm3 for pharmacodynamics study (31 days after injection) were sorted into treatment groups with similar mean tumor volumes.  Tazemetostat or vehicle (0.5% methyl cellulose + 0.1% Tween-80 in water) was administered at the indicated doses on twice a day schedules for either 7 or 28 days by oral gavage.  As reference compound, doxorubicin HCl in saline was dosed at 10 mg/kg.  Each dose was delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals.  Mice were monitored for overall health status daily and their tumor volumes were monitored twice a week using a digital caliper throughout the experiment.  On day 7 (pharmacodynamics study) or day 28 (efficacy study), mice were sampled in a prespecified fashion.  Sampling included nonterminal bleeds (0.15 mL) from the retro-orbital venous plexus with anesthesia by isoflurane inhalation.  Fuji xenograft studies were performed at Eisai Tsukuba.  The protocols were approved by the IACUC of Eisai Tsukuba (Permit Number: 13-D-0307-002 for efficacy study and 14-D-0047-001 for pharmacodynamics study).  Fuji cells were harvested during mid-log phase growth, and resuspended in HBSS with 50% Matrigel.  Balb/C-nu mice received 1 × 107 cells (0.1 mL cell suspension) subcutaneously in the right flank.  Mice carrying tumors of approximately 200 mm3 for efficacy study (25 days after injection) or 260 mm3 for pharmacodynamics study (26 days after injection) were sorted into treatment groups with similar mean tumor volumes.

extract_protocol:
RNA extraction was performed as previously described Knutson SK, Wigle TJ, Warholic NM, Sneeringer CJ, Allain CJ, et al. (2012) A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells. Nat Chem Biol 8: 890-896.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina RS-122-2103).  Briefly, Total RNA samples are concentration normalized, and polyadenylated RNA is purified using oligo-dT attached to magnetic beads.  Purified mRNA is fragmented using heat in the presence of divalent cations. Fragmented RNA is converted into double-stranded cDNA, with dUTP utilized in place of dTTP in the second strand master mix.  A single 'A' base is added to the cDNA and forked adaptors that include index, or barcode, sequences are attached via ligation. The resulting molecules are amplified via polymerase chain reaction (PCR). During PCR the polymerase stalls when a dUTP base is encountered in the template. Since only the second strand includes the dUTP base, this renders the first strand the only viable template, thereby preserving the strand information.  Final libraries are quantified, normalized and pooled.  Pooled libraries are bound to the surface of a flow cell and each bound template molecule is clonally amplified up to 1000-fold to create individual clusters.  Four fluorescently labeled nucleotides are then flowed over the surface of the flow cell and incorporated into each nucleic acid chain.  Each nucleotide label acts as a terminator for polymerization, thereby ensuring that a single base is added to each nascent chain during each cycle.  Fluorescence is measured for each cluster during each cycle to identify the base that was added to each cluster. The dye is then enzymatically removed to allow incorporation of the next nucleotide during the next cycle.

treatment_protocol: Fuji xenograft studies were performed at Eisai Tsukuba.  Tazemetostat, EPZ011989 or vehicle (0.5% methylcellulose + 0.1% Tween-80 in water) was administered at the indicated doses on twice a day schedules for either 7, 29 or 35 days by oral gavage.  Each dose was delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals.  Mice were monitored for overall health status daily during the dosing period or twice a week after the dosing period, and their tumor volumes were monitored twice a week using a digital caliper throughout the experiment. PDX studies (CTG-0771, CTG-0331, and CTG-1169) were performed at Champions Oncology.  The protocols were approved by the IACUC of Champions Oncology (Permit Number:  CHA-003-2013).  Tumor fragments (5 mm x 5 mm x 5 mm) were harvested from donor animals, each implanted from a specific passage lot (CTG-0331 and CTG-0771 at P4).  NCr-nu mice (Taconic) received the fragment subcutaneously in the flank region.  Mice carrying tumors of approximately 100-300 mm3 were sorted into treatment groups with similar mean tumor volumes.  Tazemetostat or vehicle (0.5% sodium carboxymethylcellulose +0.1%Tween-80 in water) was administered at the indicated doses on twice a day schedules for 35 days by oral gavage.  As reference compound, doxorubicin HCl in saline was dosed at 3 mg/kg.  Each dose was delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals.  Mice were monitored for overall health status daily and their tumor volumes were monitored twice a week using a digital caliper throughout the experiment.  For the CTG-0771 and CTG-0331 models, 3 to 5 mice per group with the largest tumors were euthanized by carbon dioxide inhalation on day 35 for blood and tissue sampling, and the 7 remaining mice were followed for an additional 25 days as animal survival study.  Analgesics and anesthetics were not administered.  Mice were humanely euthanized by carbon dioxide inhalation if their body weights dropped more than 20% of the original weight for two consecutive measurements, more than 30% of the original weight for one measurement, their xenograft tumor grew larger than 2000 mm3, or they showed appear moribund at any time, while a tumor volume endpoint in Kaplan-Meier survival curve was 1200 mm3, with the exception of the slower growing CTG-1169 model for which 600 mm3 was used as an endpoint for Kaplan-Meier survival curve  Diet gel was provided ad libitum if their body weights dropped more than 10%.  The summary of deaths for the 3 models is as follows:  For CTG-0771 there was one animal found dead in 400-500 mg/kg group.  For CTG-0331 there was no dead animal.  For CTG-1169 there were four animals that were found dead in multiple groups, two animals in 125 mg/kg group, one animal in 500 mg/kg group, and one animal in doxorubicin group.  For the above cases, necropsies were performed and the causes of death were not clarified.

tag: model

value: Fuji Xenograft model

tag: cell or tumor type

value: synovial sarcoma

tag: xenograft or pdx

value: xenograft

tag: treatment time (days)


title: Fuji  Vehicle 7 day treatment BID 7Fuji-1_L4.D707


title: Fuji  250mg/kg Tazemetosta 35 day treatment BID 35Fuji-9_L3.D703


title: JIA patient 13_clinical_remission

city: BUFFALO

first: JAMES

last: JARVIS

state: NY

address: 875 ELLICOTT STREET 8026

department: PEDIATRIC

institute: UNIVERSITY AT BUFFALO

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_2

data_processing:
Sequences were excluded for adapter contamination and low quality bases
Sequences were aligned to hg19 human reference genome using Tophat version 2.0.13
Gene expression abundance was calculated by HTSeq count version 0.6.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each sample

source_name: CD4+ T cell

extract_protocol:
Total RNA was extracted using TRIzol™ reagent according to manufacturer's directions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA). RNA was quantified spectrophotometrically (Nanodrop, Thermo Scientific, Wilmington, DE) and assessed for quality by capillary gel electrophoresis (Agilent 2100 Bioanalyzer; Agilent Technologies, Inc., Palo Alto, CA)
Samples libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit according to the manufacture's recommended protocols

tag: disease stage

tag: tissue

value: blood

tag: cell type

value: CD4+ T cell


title: JIA patient 10_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_10


title: JIA patient 12_clinical_remission

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_1


title: JIA patient 9_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_9


title: Fuji  Vehicle 35 day treatment BID 35Fuji-4_L2.D710


title: Fuji  Vehicle 35 day treatment BID 35Fuji-6_L2.D712


title: Fuji  Vehicle 35 day treatment BID 35Fuji-7_L3.D701


title: JIA patient 8_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_8


title: Fuji  Vehicle 35 day treatment BID 35Fuji-5_L2.D711


title: JIA patient 7_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_7


title: JIA patient 6_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_6


title: Fuji  Vehicle 35 day treatment BID 35Fuji-3_L2.D709


title: Fuji  500mg/kg Tazemetosta 35 day treatment BID 35Fuji-20_L5.D701


title: Fuji  Vehicle 35 day treatment BID 35Fuji-2_L2.D708


title: JIA patient 4_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_4


title: JIA patient 14_clinical_remission

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_3


title: Fuji  500mg/kg Tazemetosta 35 day treatment BID 35Fuji-17_L4.D711


title: JIA patient 3_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_3


title: Fuji  250mg/kg Tazemetosta 35 day treatment BID 35Fuji-8_L3.D702


title: Fuji  500mg/kg Tazemetosta 35 day treatment BID 35Fuji-19_L4.D712


title: Fuji  500mg/kg Tazemetosta 35 day treatment BID 35Fuji-15_L4.D709


title: JIA patient 2_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_2


title: JIA patient 5_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_5


title: JIA patient 11_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_11


title: JIA patient 1_active_disease

description:
JIA patient with active, untreated disease
CD4TCell_ADT_1


title: Fuji  250mg/kg Tazemetosta 35 day treatment BID 35Fuji-14_L4.D708


title: Fuji  250mg/kg Tazemetosta 35 day treatment BID 35Fuji-13_L4.D707


title: Fuji  250mg/kg Tazemetosta 35 day treatment BID 35Fuji-10_L3.D704


title: Fuji  500mg/kg Tazemetosta 35 day treatment BID 35Fuji-21_L5.D702


title: Fuji  250mg/kg Tazemetosta 35 day treatment BID 35Fuji-11_L3.D705


title: Fuji  250mg/kg Tazemetosta 35 day treatment BID 35Fuji-12_L3.D706


title: Fuji  Vehicle 35 day treatment BID 35Fuji-1_L2.D707


title: CTG-0771 Vehicle 35 day treatment BID 0771-4_L7.D704

source_name: CTG-0771, Champions Oncology

value: CTG-0771, Champions Oncology

value: PDX


title: CTG-0771 Vehicle 35 day treatment BID 0771-5_L7.D705


title: CTG-0771 400/500 mg/kg Tazemetostat 35 day treatment BID 0771-8_L1.D708_508


title: CTG-0771 400/500 mg/kg Tazemetostat 35 day treatment BID 0771-6_L7.D706


title: CTG-0771 400/500 mg/kg Tazemetostat 35 day treatment BID 0771-7_L1.D707_508


title: CTG-0331 400mg/kg Tazemetostat 35 day treatment BID 0331-9_L6.D711

source_name: CTG-0331, Champions Oncology

value: CTG-0331, Champions Oncology


title: CTG-0331 400mg/kg Tazemetostat 35 day treatment BID 0331-8_L6.D710


title: Fuji  500mg/kg Tazemetosta 35 day treatment BID 35Fuji-16_L4.D710


title: CTG-0771 Vehicle 35 day treatment BID 0771-2_L7.D702


title: CTG-0771 Vehicle 35 day treatment BID 0771-3_L7.D703


title: CTG-0331 400mg/kg Tazemetostat 35 day treatment BID 0331-7_L6.D709


title: CTG-0331 Vehicle 35 day treatment BID 0331-4_L5.D706


title: Fuji  250mg/kg Tazemetosta 7 day treatment BID 7Fuji-13_L6.D707


title: CTG-0331 400mg/kg Tazemetostat 35 day treatment BID 0331-6_L6.D708


title: CTG-0331 Vehicle 35 day treatment BID 0331-2_L5.D704


title: CTG-0331 Vehicle 35 day treatment BID 0331-3_L5.D705


title: CTG-0331 Vehicle 35 day treatment BID 0331-1_L5.D703


title: CTG-0331 Vehicle 35 day treatment BID 0331-5_L6.D707


title: Otiwi1 RIP-seq 19h

city: Washington

first: John

middle: Russell

last: Bracht

state: DC

address: 4400 Massachusetts Ave NW

department: Biology

institute: American University

data_processing:
Reads from fusion backcross (otiwi_chip_TEBPb-contig11396_fusion_backcross.fastq) and WT (19h_IP.fa) were mapped with SRiMP to germline reference (C1929818.fasta) using this command line: gmapper -Q -N 8 -h 80% <input_reads> C1929818.fasta
SAM output was visualized in Geneious and figure generated for publication.
Supplementary_files_format_and_content: sam

organism: Oxytricha trifallax

source_name: whole cell

growth_protocol: Standard ciliate growth on Chlamydomonas reinhardtii food supplemented with K. pneumoniae, in Pringsheim culture media

extract_protocol:
live cells fixed with 1% formaldehyde and then processed as outlined in Fang et al. 2012, Cell 151, 1243-1255
standard Illumina small RNA construction after reversal of crosslinks

treatment_protocol: Chromosome fusion created previously by microinjection, and was stably maintained prior to backcross to JRB510

tag: genotype

value: cells containing fusion chromosome backcross to wildtype JRB510


title: WT GS 18h-H3R17me2_ChIPSeq

status: Public on Jun 17 2016

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7 using option of --best -v 2 --strata -m 1
bedgraph files were generated using Homer using tbp -1 option
genome build: mm9
processed data files format and content: bedgraph

molecule: genomic DNA

organism: Mus musculus

growth_protocol: MEFs were cultured in DMEM+10% FBS(Gibco)+Antibiotics at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
For ChIP experiments, cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3R17me2 antibody.
ChIP-seq libraries were prepared for sequencing using the NEXTflex ChIP-seq kit, according to the manufacturer's instructions

treatment_protocol: For glucose starvation, cells were washed with PBS, then incubated with glucose-free DMEM supplemented with 10% dialyzed FBS.

tag: strain

tag: passages

value: 3 to 5

value: Embryonic Fibroblast

value: wildtype

tag: chip antibody


title: CTG-0771 Vehicle 35 day treatment BID 0771-1_L7.D701


title: WT 0h-H3R17me2_ChIPSeq


title: WT 0h-input_ChIPSeq

value: none (input)


title: WT GS 18h-input_ChIPSeq


title: Carm1 KO-GS 18h-rep.2_RNA-seq

description: processed data file: gene.count.txt

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using Tophat2 (v2.0.9).
bedtools was used to get read counts for genes (bedtools multicov -split -D)
genome build: mm9
processed data files format and content: text file with read counts obtained for each sample for RNAseq data

extract_protocol:
RNA were harvested using Trizol and RNA were extracted using Qiagen Rneasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Carm1 KO


title: Carm1 KO-GS 18h-rep.1_RNA-seq

description: processed data file: gene.count.txt


title: Carm1 KO 0h-rep.2_RNA-seq

description: processed data file: gene.count.txt


title: WT 0h-rep.2_RNA-seq

description: processed data file: gene.count.txt


title: WT-Glucose Starvation(GS) 18h-rep.1_RNA-seq

description: processed data file: gene.count.txt


title: CTG-0331 400mg/kg Tazemetostat 35 day treatment BID 0331-10_L6.D712


title: WT-Glucose Starvation(GS) 18h-rep.2_RNA-seq

description: processed data file: gene.count.txt


title: Carm1 KO 0h-rep.1_RNA-seq

description: processed data file: gene.count.txt


title: WT 0h-rep.1_RNA-seq

description: processed data file: gene.count.txt


title: Experimental Sample_siUpf1_1

city: La Jolla

first: Heidi

last: Cook-Andersen

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

data_processing:
RNA-seq reads were mapped with the STAR pipeline against hg19 transcriptome hosted at TSCC.
The python script rpkmforgenes.py was used to quantify counts for each gene and DESeq2 was used to calculate differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes raw reads and RPKM values for each Sample.

source_name: Experimental Sample_siUpf1

growth_protocol: H9 hESCs were cultured on Matrigel-coated plates in DMEM/F12 media supplemented with E8.

extract_protocol:
RNA was isolated with Trizol and total RNA quality was assessed using an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siControl or siUPF3A we used.  24 h after transfection, cells were treated with actinomycin D and RNA was isolated 0, 15, 105, and 225 minutes post-actinomycin D treatment.

tag: cell line

value: hESCs

tag: treated with


title: Control Sample_siLuc_2

source_name: Control Sample_siLuc

value: Control siLuc


title: Experimental Sample_siUpf1_2


title: Control Sample_siLuc_1


title: input_DNA

city: Stanford

first: Gill

last: Bejerano

address: 279 Campus Drive West (MC 5329)

department: Developmental Biology

institute: Stanford University

description: timed pregnant mice from Charles River

data_processing:
Sequencing reads were mapped to the mouse reference genome (NCBI37/mm9) using version 0.7.12-r1039 of the BWA sampe and aln mapping algorithms with default parameters.
ChIP-seq quality was assessed using phantompeakqualtools version 2.0 (https://code.google.com/p/phantompeakqualtools/) and all replicates received the highest quality score.
Input samples were merged.
Peaks were called using MACS version 2.1.0 20140616 with a p-value cutoff of 0.01 and merged using the Irreproducible Discovery Rate (IDR) framework October 2010 version using a threshold of 0.01 as previously described (https://sites.google.com/site/anshulkundaje/projects/idr).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS2; Scores represent signal per million reads for fragment pileup profiles.

source_name: Whole cortex dissected from embryonic day 15.5 (E15.5) embryos

extract_protocol:
Cortices dissected from E15.5 embryos were fixed for 10 min with 1% formaldehyde and neutralized with glycine. The cells were lysed and the chromatin was sheared into ~300 base pair (bp) fragments.
Libraries were generated from the ChIP-ed DNA and input DNA using the Illumina TruSeq kit according to the manufacturer's protocol.

value: brain cortex

tag: developmental stage

value: embryonic day 15.5


title: C2C12 undifferentiated LaminB1-Dam

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: C2C12 undifferentiated LaminB1-Dam

data_processing:
Basecalls and quality filtering performed by BGI according to their standard procedures
Clean reads were aligned to the mouse mm9 genome using the Burrows-Wheeler aligner bwa mem. Mitochondrial sequences (a common contaminant in these experiments) and unaligned reads were filtered out (output: ffSE_xx_mm9.bam files).
Reads were counted per DpnI fragment (genomic sequence flanked by GATC motifs), and log2(ratio LaminB1/dam) measurements were obtained for undifferentiated and differentiated samples. The log2 ratios were then normalised using quantile normalisation (Bioconductor Limma package) and converted to bigwig format for visualisation purposes.
To identify LADs, the peakfinder software SICER (v1.1) was employed with the following parameters: redundancy threshold 1, window size 500bp, gap size 0, fragment size 150bp, effective genome fraction 0.75, FDR 0.05
IP and PI regions were then identified by comparing the mean intensity differences between MT (differentiated C2C12) and MB (undifferentiated C2C12)  log2(Lamin B1/Dam) values along a running 100 kb window. Regions with a mean MT/MB lamin B1 signal difference of 2 fold were then tested for significance against a randomized signal sample population using Fisher's exact test over 1,000 iterations. Regions with a P>0.01 were disregarded
Genome_build: mm9
Supplementary_files_format_and_content: sqq3_U.bw contains the DamID data for C2C12 undifferentiated as log2(LaminB1/dam control), per DpnI fragment, quantile normalised.
Supplementary_files_format_and_content: sqq3_D.bw contains the DamID data for C2C12 differentiated for 6 days as log2(LaminB1/dam control), per DpnI fragment, quantile normalised.
Supplementary_files_format_and_content: ffSE_32_mm9-W500-G0-FDR0.05-island.bed contains the coordinates of LaminB1 DamID peaks for C2C12 undifferentiated, obtained with SICER
Supplementary_files_format_and_content: ffSE_35_mm9-W500-G0-FDR0.05-island.bed contains the coordinates of LaminB1 DamID peaks for C2C12 differentiated (6 days), obtained with SICER
Supplementary_files_format_and_content: 150811_0.01_DR_U.bed contains the coordinates of differential regions (DR) that appear more associated with the nuclear envelope in the undifferentiated state (PI regions)
Supplementary_files_format_and_content: 150811_0.01_DR_D.bed contains the coordinates of differential regions (DR) that appear more associated with the nuclear envelope in the differentiated state (IP regions)

source_name: myoblast

growth_protocol: C2C12 Myoblasts (MBs) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 20% fetal calf serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin and passaged every 2 days in a 1:7 dilution by trypsinisation. Critically, cells were never permitted to reach more than 80% confluency, i.e. ~2.5 million cells on an 8.5 cm diameter tissue culture plate.

extract_protocol:
Genomic DNA was extracted using Qiagen DNA-Easy kit, following manufacturer's instructions.
Libraries were prepared by Beijing Genomics Institute (BGI) to Illumina's specifications
DamID

treatment_protocol:
Myoblasts were induced to differentiate at 48h post-confluency by starvation using medium with 2% horse serum. Differentiation media was replaced every 48h up to 144h post-induction. To inhibit contraction 1uM tetrodotoxin was added at 96h post-induction,
Lentivirus encoding the control Dam, or LaminB1-Dam fusion, was used to transduce untreated myoblasts or differentiated myoblasts at 72h post-induction. Transduction was allowed for 24h. At 72h post-transduction genomic DNA was extracted.
Dam-methylated genomic DNA was enriched using the standard protocol as described by Vogel et al. (2007) Nature Protocols 2:1467-1478. It involves digesting gDNA with DpnI enzyme, which cuts at non-Adenine-methylated GATC motifs.

tag: treatment

value: untreated

tag: damid


title: C2C12 undifferentiated Dam control

description: C2C12 undifferentiated Dam control

value: Dam


title: C2C12 differentiated Dam control 1

description: C2C12 differentiated Dam control

value: differentiated


title: Cont15 RNA-seq

status: Public on Jun 16 2016

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

description:
Directional RNA-seq on rRNA depleted RNA
JG95

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (ELAND - 1.7.0).  Initial data processing was performed using the default read length of 100 bp.
Illumina Casava was used for basecalling.
After the sequence data was obtained from Illumina HiSeq 2500, we we used gsnap (ver 2012-05-07)  for the alignment and htseq (v0.5.3p3) for counting transcripts. The alignment and counting transcripts were performed using automated WASP pipeline (WASP-3.1.3 (ref. 6589)).
Genome_build: hg19
Supplementary_files_format_and_content: Format: txt; files were generated using in house pipeline; Scores represent expression count with ensemble gene IDs

source_name: Amnion

extract_protocol:
Total RNA was extracted using TRIzol reagent from amnion membrane and the total RNA was then treated with DNaseI to eliminate residual DNA.
The 500 ng of extracted RNA samples were subjected to directional RNA seq library preparation. We eliminated ribozomal-RNA (rRNA) from total RNA with RiboZero kit (Illumina)  before reverse transcription with the SuperScript III kit (Invitrogen) using oligo-d(T) and random hexamers. The second strand cDNA was synthesized with dUTP. After the second strand synthesis, the products were fragmented, end-repaired, dA tailed and added Illumina sequencing adapters. Before PCR amplification, we treated the product with Uracil-DNA glycosylase.

tag: clinical information

value: Control

tag: gender

value: Female

tag: tissue type

value: Amnion


title: Cont14 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG93

value: Male


title: PE36 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG03

value: Preeclampsia


title: Cont11 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG75


title: Cont12 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG90


title: PE33 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG73


title: PE25 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG56


title: PE27 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG58


title: PE17 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG40


title: PE24 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG55


title: PE31 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG63


title: Cont8 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG43


title: PE11 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG33


title: Tbr1_ChIPSeq

description: timed pregnant mice from Charles River

value: Rabbit anti TBR1 (Abcam) antibody


title: C2C12 differentiated Dam control 2

description: C2C12 differentiated Dam control


title: PE10 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG32


title: Unlesioned/Saline Treated 5

city: Birmingham

first: David

last: Figge

state: AL

address: 1719 6th Ave. S, CIRC 520

department: Neurology

institute: University of Alabama-Birmingham

description:
Bisulfite Converted Genomic DNA
Unlesioned/Saline Treated

data_processing:
Bisulfite conversion efficiency was greater that 98% for all of the samples and we obtained an average of 68 million reads per library. Quality control on raw reads was performed with FastQC (version 0.10.1, http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc), and adaptor trimming and removal of trimmed reads shorter than 20 bp was performed with Trim Galore (version 0.3.7, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
Trimmed reads were mapped to the UCSC Rattus norvegicus rn5 genome with the methylation-aware mapper bismark (version 0.13.0). Samtools (version 0.1.19–96b5f2294a) used to sort SAM files produced by bismark and de-duplicate reads. SAM files were analyzed using MethylKit (version 0.9.2) in R (Akalin et al., 2012).
Genome_build: Rn5
Supplementary_files_format_and_content: tab delimited text files containing CpG methylation info for all analyzed cytosines including chromosome, base pair, strand, coverage, frequency of methylated cytosine, frequency of bisulfite coverted cytosine to thymidine

organism: Rattus norvegicus

source_name: Dorsal Striatum

extract_protocol:
Rats were given a unilateral dopaminergic lesion to the left medial forebrain bundle with 6-OHDA to destroy at least 90% of TH positive axons.  Animals were allowed to recover for 3 weeks and then given daily injections of L-DOPA (6 mg/kg) for seven days to establish stable dyskinesia. Animals were sacked 3 hrs following the final L-DOPA injection and the dorsal striatum was immediately dissected and flash frozen
One μg of gDNA sample was used for library construction. Bisulfite converted DNA libraries were produced and adaptor ligated, and 50 bp single-end reads were sequenced on an Illumina HiSeq-2500 following library QC and analyzed using Illumina Casava 1.8.

value: Sprague Dawley

value: Brain/Dorsal Striatum

tag: age

value: 120 days

value: Wild Type


title: PE8 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG30


title: Unlesioned/Saline Treated 1


title: PE9 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG31


title: PE7 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG29


title: PE6 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG28


title: Unlesioned/Saline Treated 4


title: Lesioned/Saline Treated 8

description:
Bisulfite Converted Genomic DNA
Lesioned/Saline Treated


title: Lesioned/L-DOPA Treated 6

description:
Bisulfite Converted Genomic DNA
Lesioned/L-DOPA Treated


title: Lesioned/Saline Treated 7


title: Cont9 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG69


title: Unlesioned/Saline Treated 6


title: PE4 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG20


title: PE16 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG39


title: Cont6 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG21


title: Unlesioned/Saline Treated 3


title: Cont4b RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG08b


title: PE2 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG18


title: Lesioned/L-DOPA Treated 2


title: Cont3 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG06


title: PE1 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG01


title: Cont4 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG08


title: Lesioned/L-DOPA Treated 1


title: Unlesioned/Saline Treated 2


title: Lesioned/L-DOPA Treated 3


title: PE36 HELP-tagging

description:
HpaII test for HELP-tagging
JG03

data_processing:
Library strategy: HELP-tagging
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (ELAND - 1.7.0).  Initial data processing was performed using the default read length of 37 or 42 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions. To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Illumina Casava was used for basecalling.
After the sequence data was obtained from Illumina HiSeq 2500, we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again  (ELAND - 1.7.0) on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: Format: txt; The angle files were generated using in house pipeline; Scores represent degree of unmethylation. tid: ID for reference, chr: chromosome, pos: position of HpaII site, angle: degree of DNA hypomethylation, conf: degree of confidence, higher values have higher confidency

extract_protocol:
High molecular weight genomic DNA was extracted from amnion.
Custom adapters were created for HELP-tagging, referred to as AE and AS Index. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence, and adapter AS contains index sequences for multiplexing .  Adapter AS contains an Illumina sequencing primer sequence. Three to five micrograms of genomic DNA were digested with HpaII in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure XP (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired and tailed with a single dA at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the PCR purification kit (Zymo Research) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription with the SuperScript III kit (Invitrogen) using custom primer.  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a PCR clean-up kit (Zymo Research).


title: Lesioned/L-DOPA Treated 5


title: Lesioned/L-DOPA Treated 7


title: Lesioned/L-DOPA Treated 4


title: Cont7 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG25


title: Cont2 RNA-seq

description:
Directional RNA-seq on rRNA depleted RNA
JG05


title: Cont14 HELP-tagging

description:
HpaII test for HELP-tagging
JG93


title: Cont13 HELP-tagging

description:
HpaII test for HELP-tagging
JG91


title: Lesioned/Saline Treated 6


title: Lesioned/Saline Treated 4


title: Hypertension11 HELP-tagging

description:
HpaII test for HELP-tagging
JG88

value: Hypertension


title: Lesioned/Saline Treated 3


title: PE34 HELP-tagging

description:
HpaII test for HELP-tagging
JG80


title: Cont11 HELP-tagging

description:
HpaII test for HELP-tagging
JG75


title: Cont12 HELP-tagging

description:
HpaII test for HELP-tagging
JG90


title: Lesioned/Saline Treated 2


title: Lesioned/Saline Treated 5


title: Cont10 HELP-tagging

description:
HpaII test for HELP-tagging
JG74


title: Lesioned/Saline Treated 1


title: PE33 HELP-tagging

description:
HpaII test for HELP-tagging
JG73


title: PE35 HELP-tagging

description:
HpaII test for HELP-tagging
JG82


title: PE31 HELP-tagging

description:
HpaII test for HELP-tagging
JG63


title: PE32 HELP-tagging

description:
HpaII test for HELP-tagging
JG64


title: July06_UnPoll

city: Vancouver

first: Juergen

last: Ehlting

state: BC

address: 321 - 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

data_processing:
Reads were delivered in BAM files that were converted to paired-end FASTQ files with the bamToFastq tool from the BEDTools package v 2.17. These FASTQ files were evaluated for base quality, nucleotide overrepresentation, and sequence overrepresentation using FastQC v0.10. The quality scores and sequence overrepresentation data were used to direct read trimming. Reads were trimmed with TrimGalore! v0.2. A minimum Phred cut-off of 20 was used for quality trimming. Built-in adapter trimming was used to remove Illumina sequencing artifacts. Reads were discarded that were shorter than 36 bp after trimming or whose mates were removed due to trimming. To confirm that Illumina adapter sequences and low quality bases were removed after trimming, the data for each library were reassessed with FastQC.
Trimmed FASTQ reads were mapped to a filtered reference assembly generated from the reads using Bowtie 1.0.1 and counted using RSEM 1.2.12. First, the reference FASTA file was prepared for RSEM using rsem-prepare-reference. The mapped reads were used to calculate estimated coverage counts using rsem-calculate-expression.
Inter-library normalization was calculated with R 3.1.0 using the Bioconductor package cqn 1.10.0. Library size and GC-content were used as normalizing factors. Sequence length was not incorporated into the calculation because it is accounted for in RSEM count estimates. Resulting FPKM-values were lifted by adding a value of 1 and log2-transformed. Only transcripts with an FPKM value greater than one were retained, for a total of 54,489 transcripts.
Genome_build: TSA submission: GAZW00000000.2
Supplementary_files_format_and_content: Tab delimited data matrix with column one containing transcript IDs as in TSA submitted and columns two to eleven containing expression data (lifted, log2-transformed FPKM values).

molecule: polyA RNA

organism: Pseudotsuga menziesii

source_name: Megagametophyte, not pollinated, 06. July 2011

growth_protocol: Several ramets of a single genotype clone of Pseudotsuga menziesii, genotype 970, were grown in the field in the Mount Newton seed orchard (TimberWest Inc.), Saanichton, British Columbia, Canada.

extract_protocol:
Extraction of total RNA was performed using a method modified from Kolosova et al. (2004). 200 mg to 400 mg of ground tissue was used. Total RNA was DNAse treated.
PolyA-plus RNA, library construction, and sequencing was performed at the Michael Smith Genome Sciences Centre in Vancouver, Canada. Four indexed libraries were pooled per lane for sequencing on an Illumina HiSeq2000 sequencer. The non strand specific paired-end reads were 100 bp in length with target insert sizes ranging between 200 and 300 bp.

treatment_protocol: Prior to anthesis (April 19th), branches were manually emasculated and covered with paper exclusion bags to prevent pollination. In all, 389 seed cones were isolated for this study. At the time of pollen receptivity (May 9th), half of these bags were randomly chosen to have pollen introduced using the orchard’s standard mix of pollen from six different genotypes; this mix is known to produce viable embryos across many genotypes The remaining bags were left unpollinated. After pollen production in the orchard ceased (May 20th), the paper pollen exclusion bags were removed and replaced with mesh bags for the duration of the experiment to prevent insect damage.   Cones were collected and dissected (200–400 megagametophytes per treatment) on four dates: June 10, June 22, June 30, and July 6. These dates coincided with key events in seed development. In order, these events are corrosion cavity formation, fertilization, embryogenesis, or the early stages of abortion in the unpollinated treatment. Isolated megagametophytes and vegetative tissue (i.e. bracts and scales collected on May 26, also from orchard grown genotype 970) were immediately flash-frozen in liquid nitrogen, then stored in at -80 °C.

value: Megagametophyte

tag: date


title: Bracts

source_name: Bracts from developing cones, May 26 2011

value: Sporophyte, developing cone, cone bracts


title: Cont9 HELP-tagging

description:
HpaII test for HELP-tagging
JG69


title: Cont15 HELP-tagging

description:
HpaII test for HELP-tagging
JG95


title: PE29 HELP-tagging

description:
HpaII test for HELP-tagging
JG61


title: Scales

source_name: Whole scales from developing cones, May 26 2011

value: Sporophyte, developing cone, cone scales


title: n_WT_dmso-minus-4-thiouracil

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

description:
nascent RNA
5 uM

data_processing:
Base calls were performed with CASAVA-1.8.2.
Reads were clipped of 3' adapters and aligned to concatenated SacCer3 from SGD and ASM294v.2.23 from PomBase with STAR 2.3.0 using default settings except reads mapping to more than one locus were discarded to prevent ambiguous alignment of sequences shared between species.
Read counts for genes were obtained using HTSeq 0.6.0 using default parameters.
Genome_build: SacCer3 and ASM294v.2.23
Supplementary_files_format_and_content: tab-delimited text file of pre-normalized read counts for S. cerevisiae and S. pombe genes

organism: Saccharomyces cerevisiae

source_name: yeast BY4741

growth_protocol: Yeast were grown in His-dropout media + 2% dextrose at 30 °C in a shaking incubator from an OD600 of 0.1 to mid-log phase OD600 of 0.5 to 1.

extract_protocol:
Total RNA was extracted using the Yeast RiboPure RNA Purification Kit (Life Technologies, AM1926). Before lysis, S. pombe cells were added in a 1:6 pombe-to-cerevisiae cellular ratio. Pombe cells were also labeled with 4-thiouracil. For nascent RNA extraction, 100 ug of total RNA was biotinylated with 200 ug of Biotin-HPDP (Pierce, #21341), and the labeled RNA was purified using the uMacs Streptavidin Kit (Miltenyi, #130-074-101).
Both total and nascent RNA were ribosomal RNA-depleted and prepared for sequencing using the Yeast ScriptSeq Complete Gold Kit (Epicentre, BGY1324). DNA was sequenced on an Illumina HiSeq 2000 generating single-end reads of 100 bp length using standard Illumina protocols.

treatment_protocol: Cells were treated with 2 or 5 uM of inhibitor (1-NAPP-1 or CMK) or equivalent solvent control (DMSO) at mid-log phase (25 mL, OD600 0.4 to 1) for 1 hr. Six minutes before harvest, cells were labeled with 5 mM 4-thiouracil.

value: wild-type

value: DMSO


title: n_kin28is_cmk-rep4

description:
nascent RNA
5 uM

value: CMK


title: PE30 HELP-tagging

description:
HpaII test for HELP-tagging
JG62


title: June22_UnPoll

source_name: Megagametophyte, not pollinated, 22. June 2011


title: PE28 HELP-tagging

description:
HpaII test for HELP-tagging
JG59


title: June30_UnPoll

source_name: Megagametophyte, not pollinated, 30. June 2011


title: n_kin28is_cmk-rep3

description:
nascent RNA
5 uM


title: June10_UnPoll

source_name: Megagametophyte, not pollinated, 10. June 2011


title: PE26 HELP-tagging

description:
HpaII test for HELP-tagging
JG57


title: n_kin28is_dmso-rep3

description:
nascent RNA
5 uM


title: July06_Poll

source_name: Megagametophyte, pollinated, 06. July 2011

value: Megagametophyte/embryo (fertilized with mixed pollen)


title: PE24 HELP-tagging

description:
HpaII test for HELP-tagging
JG55

value: Female


title: PE25 HELP-tagging

description:
HpaII test for HELP-tagging
JG56

value: Amnion


title: June30_Poll

source_name: Megagametophyte, pollinated, 30. June 2011


title: PE27 HELP-tagging

description:
HpaII test for HELP-tagging
JG58

value: Male


title: n_kin28is_cmk-rep2

description:
nascent RNA
5 uM


title: Hypertension10 HELP-tagging

description:
HpaII test for HELP-tagging
JG65


title: June22_Poll

source_name: Megagametophyte, pollinated, 22. June 2011


title: PE23 HELP-tagging

description:
HpaII test for HELP-tagging
JG54

value: Preeclampsia


title: Adult_retina_runoff_negative

first: Christine

middle: E

last: Holt

address: Anatomy Bldg., Downing St.

department: Department of PDN

institute: University of Cambridge

description: Ribosome-bound mRNAs

data_processing:
The sequence reads were mapped to the mouse genome (mm10) using TopHat 2 version 2.0.12
Transcript assembly and estimation of FPKM (Fragments Per Kilobase of transcript per Million fragments sequenced) values were performed using Cufflinks version 2.2.1
Read counts for each gene were determined using HTSeq version 0.6.1p1. Four samples (AYRM, AYRP, ASRM and ASRP) contain read count values. The rest have FPKM.
Python script "bed2wig.py" was used to make wig files from sam files. https://github.com/daler/rdbio-scripts/blob/master/sequenceFiles/bed2wig.py
Genome_build: mm10
Supplementary_files_format_and_content: wig files, FPKM, and read counts

source_name: Retina

growth_protocol: We crossed the RiboTag knock-in mouse line (Sanz et al., Proc Natl Acad Sci U S A 106, 2009) with Pax6-alpha-Cre mouse (Marquardt et al., Cell 105, 2001).

extract_protocol:
Immunopurified RNAs are reverse-transcribed, and then amplified by a PCR-based method (Tang et al., Nat Methods 6, 2009).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tissues were lyzed and subjected to immunoprecipitation.

tag: development stage

value: Adult


title: Hypertension9 HELP-tagging

description:
HpaII test for HELP-tagging
JG53


title: June10_Poll

source_name: Megagametophyte, pollinated, 10. June 2011


title: n_kin28is_1napp1-rep2

description:
nascent RNA
5 uM


title: PE22 HELP-tagging

description:
HpaII test for HELP-tagging
JG51


title: Adult_cre_positive_runoff_negative

description: Ribosome-bound mRNAs

source_name: Superior colliculus


title: n_kin28is_1napp1-rep3

description:
nascent RNA
5 uM


title: Hypertension7 HELP-tagging

description:
HpaII test for HELP-tagging
JG49


title: PE21 HELP-tagging

description:
HpaII test for HELP-tagging
JG48


title: n_kin28is_dmso-rep2

description:
nascent RNA
5 uM


title: Hypertension8 HELP-tagging

description:
HpaII test for HELP-tagging
JG50


title: Adult_cre_positive_runoff_positive

description: Ribosome-bound mRNAs


title: n_WT_1napp1-rep2

description:
nascent RNA
5 uM


title: Hypertension6 HELP-tagging

description:
HpaII test for HELP-tagging
JG46


title: n_WT_cmk-rep2

description:
nascent RNA
5 uM


title: n_kin28is_cmk-rep1

description:
nascent RNA
2 uM


title: 1_002OGWU_U87_GUCY1B3

city: washington

first: haijie

last: xiao

address: 2300 eye street

department: Biochemistry

institute: george washington University

description: ChIP-seq sample

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the hg19 genome using the BWA algorithm with default settings.
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.
Intervals (= Peaks) were determined using the MACS peak finding algorithm.
The resulting histograms (genomic "signal maps") were stored in bigWig files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: 002OGWU_GUCY1B3_intervals_pvalues.xlsx: Excel file includes intervals.

source_name: U-87 MG glioma cancer cells overexpressing sGCβ1, sGCβ1 ChIP

growth_protocol: U87 cells were grown in Eagle's Minimum Essential Medium supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatins were isolated with anti-sGCβ1 antibody (Sigma G4405).
The ChIP DNA was processed into a standard Illumina ChIP-Seq library.

tag: originating cell line

value: U-87 MG

tag: tissue derivation

value: malignant glioma

value: glioma cancer cell line overexpressing sGC-beta1

value: anti-sGC-beta1 (Sigma G4405, lot 021M4843)


title: n_kin28is_1napp1-rep1

description:
nascent RNA
2 uM

tag: genotype


title: PE20 HELP-tagging

description:
HpaII test for HELP-tagging
JG47


title: Adult_retina_runoff_positive

description: Ribosome-bound mRNAs

tag: strain


title: PE19 HELP-tagging

description:
HpaII test for HELP-tagging
JG45


title: n_kin28as_dmso-rep1

description:
nascent RNA
2 uM


title: n_kin28as_1napp1-rep1

description:
nascent RNA
2 uM


title: 2_002OGWU_U87_Input

description: Input sample

source_name: U-87 MG glioma cancer cells overexpressing sGCβ1, input

tag: cell type


title: YAP-TEAD305

city: Shanghai

first: Zefeng

last: Wang

address: 320 Yueyang Road

country: China

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

data_processing:
Sequenced reads were aligned to hg19 using Bowtie v2.2.5
The EBSeq tool was used to identify differentially expressed genes in pairwise comparisons of all conditions
Genome_build: hg19
supplementary_files_format_and_content: Gene expression level of all conditions was merged to genes-merge.counts.matrix using rsem-generate-data-matrix. Scores represent expected reads count at each condition derived from rsem-calculate-expression

source_name: Lung carcinoma cells

growth_protocol: The H157 lung carcinoma cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNAs were purified from  cells  using Trizol method and subsequently cleaned using RNAeasy Kit.
Total RNA not exceeding 3 μg was further used to purify polyadenylated RNA using Illumina TruSeq Total RNA Sample Prep kits.  We used the Ribo-Zero Human to remove cytoplasmic rRNA. The mRNA purified was further analyzed using Bioanalyzer (Agilent Technologies) prior to generation of cDNA library with bar coded ends. RNA-seq libraries were robotically prepared with Illumina TruSeq Total RNA Sample Prep kits according to the manufacturer’s protocol.

treatment_protocol: The H157 lung carcinoma cells stably expressing different construct were collected after reaching mid-log growth phase, then subject to RNA purification

value: Lung carcinoma cells

tag: genotype/variation

value: expressing YAP-TEAD305


title: YAP-RBM4

tag: cell line

value: expressing YAP-RBM4


title: Cont8 HELP-tagging

description:
HpaII test for HELP-tagging
JG43

source_name: Amnion

value: Control


title: n_kin28is_dmso-rep1

description:
nascent RNA
2 uM


title: Hypertension5 HELP-tagging

description:
HpaII test for HELP-tagging
JG44

value: Hypertension


title: n_WT_cmk-rep1

description:
nascent RNA
2 uM

value: wild-type


title: YAP-TEAD434

value: expressing YAP-TEAD434


title: pCDNA-ctl

value: expressing pCDNA-ctl


title: YAP

value: expressing YAP


title: PE18 HELP-tagging

description:
HpaII test for HELP-tagging
JG42

value: Female

value: Amnion


title: n_WT_dmso-rep1

description:
nascent RNA
2 uM

value: DMSO


title: PE17 HELP-tagging

description:
HpaII test for HELP-tagging
JG40

value: Preeclampsia


title: kin28is_cmk-rep2

description: 5 uM

value: CMK


title: Hypertension4 HELP-tagging

description:
HpaII test for HELP-tagging
JG41

value: Male


title: n_WT_dmso-rep2

description:
nascent RNA
5 uM


title: mRNA-seq WT3

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
For Ribo-seq analysis, Adapters were removed, and Ribo-seq reads were initially aligned to a collection of rRNA sequences to filter rRNA reads in the libraries; and non-rRNA reads with at least 23 nt length were kept. To obtain only high-confidence assignments of ribosome footprints to transcripts, the reads were aligned to the mouse reference genome (GRCm38/UCSC mm10) with Tophat2 (version: 2.1; options: ‘--read-mismatch 1 --max-multihits 1 –GTF’) guided by ENSEMBL gene models to account for splice sites, allowing one mismatch per read and unique alignments only.
For RNA-seq analysis, the reads were aligned to the mouse reference genome (GRCm38/UCSC mm10) with Tophat2 (version: 2.1; options: ‘--read-mismatch 1 --max-multihits 1 –GTF’) guided by ENSEMBL gene models allowing one mismatch per read and unique alignments only.
Genome_build: GRCm38/UCSC mm10
Supplementary_files_format_and_content: Processed data files were generated with bedtools genomeCoveragBed showing counts per genomic position.

source_name: mouse skin squamous tumours

extract_protocol:
1 cm2 pieces of skin papilloma were snap-frozen in liquid N2 and then transferred to lysis buffer.
RNAs were prepared for Ribo-seq as in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534-1550, doi:10.1038/nprot.2012.086 (2012). For mRNA-seq standard Illumina library preparation protocols were used.

tag: tumour stage

value: skin papilloma

value: 1 month


title: mRNA-seq NSun2 -/- 3


title: n_WT_1napp1-rep1

description:
nascent RNA
2 uM


title: mRNA-seq WT2


title: mRNA-seq NSun2 -/- 2


title: PE16 HELP-tagging

description:
HpaII test for HELP-tagging
JG39


title: WT_dmso-minus-4-thiouracil

description: 5 uM


title: PE15 HELP-tagging

description:
HpaII test for HELP-tagging
JG37


title: PE14 HELP-tagging

description:
HpaII test for HELP-tagging
JG36


title: PE13 HELP-tagging

description:
HpaII test for HELP-tagging
JG35


title: WT_cmk-rep2

description: 5 uM


title: Ribosome profile NSun2 -/- 2

data_processing:
Library strategy: Ribo-seq
For Ribo-seq analysis, Adapters were removed, and Ribo-seq reads were initially aligned to a collection of rRNA sequences to filter rRNA reads in the libraries; and non-rRNA reads with at least 23 nt length were kept. To obtain only high-confidence assignments of ribosome footprints to transcripts, the reads were aligned to the mouse reference genome (GRCm38/UCSC mm10) with Tophat2 (version: 2.1; options: ‘--read-mismatch 1 --max-multihits 1 –GTF’) guided by ENSEMBL gene models to account for splice sites, allowing one mismatch per read and unique alignments only.
For RNA-seq analysis, the reads were aligned to the mouse reference genome (GRCm38/UCSC mm10) with Tophat2 (version: 2.1; options: ‘--read-mismatch 1 --max-multihits 1 –GTF’) guided by ENSEMBL gene models allowing one mismatch per read and unique alignments only.
Genome_build: GRCm38/UCSC mm10
Supplementary_files_format_and_content: Processed data files were generated with bedtools genomeCoveragBed showing counts per genomic position.


title: kin28is_1napp1-rep2

description: 5 uM


title: WT_dmso-rep2

description: 5 uM


title: PE12 HELP-tagging

description:
HpaII test for HELP-tagging
JG34


title: Ribosome profile WT3


title: mRNA-seq NSun2 -/- 1


title: PE11 HELP-tagging

description:
HpaII test for HELP-tagging
JG33


title: kin28is_dmso-rep2

description: 5 uM


title: WT_1napp1-rep2

description: 5 uM


title: PE10 HELP-tagging

description:
HpaII test for HELP-tagging
JG32


title: Ribosome profile NSun2 -/- 3


title: kin28is_cmk-rep1

description: 2 uM


title: mRNA-seq WT1


title: kin28is_1napp1-rep1

description: 2 uM


title: Ribosome profile WT2


title: RNA Bisulphite sequencing NSun2 -/- 4

data_processing:
For tRNA-seq data, reads were quality-trimmed (removing bases from read ends with Q > 20)  and adapters were trimmed. Reads were aligned to the mouse reference genome (UCSC mm10) with options '-m 1 -v 2'.
For BS-seq data, reads were quality-trimmed (removing bases from read ends with Q > 20)  and adapters were trimmed. Reads were aligned with Bismark against the mouse reference genome (UCSC mm10) with options '-n 1 -l 40'.
Genome_build: GRCm28/UCSC mm10
Supplementary_files_format_and_content: For tRNA-seq data, processed data files provide bedGraph files generated by bedtools 'genomeCoverageBed' from bowtie alignments. Columns represent <chromosome> <start position> <end position> <read counts>
Supplementary_files_format_and_content: For BS-seq data, processed data files are bedGraph output files provided by Bismark. Columns represent <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

extract_protocol:
Total RNA was extracted using Trizol reagents (Invitrogen) from snap‐frozen material and treated with DNase (Turbo DNase, Ambion). Ribosomal RNA was removed using Ribo‐zero (Epicentre, Illumina).
tRNA sequencing library preparation: size‐selected or with the MirVana Isolation Kit (Invitrogen) for 20‐ to 200‐base‐paired RNAs. tRNAs were then de‐aminoacylated in 0.1 M Tris–HCl pH 9.0 and 1 mM EDTA for 30 min at 37°C. tRNA libraries were performed according to TruSeq Small RNA Preparation Kit (Illumina) instructions. Briefly, 3′ adenylated and 5′ phosphorylated adapters suitable for Illumina RNA sequencing were ligated to 300 ng of RNA obtained after de‐aminoacylation. RNA was reverse‐transcribed at 50°C for 1 h (SuperScript III cDNA synthesis kit, Invitrogen), followed by 16‐cycle PCR amplification with Phusion DNA polymerase (Thermo scientific) and size‐selected (140–210 base pairs) before sequencing. Bisulphite sequencing library preparation:  RNA was bisulphite‐converted as followed; about 2 μg of RNA was mixed in 70 μl of 40% sodium bisulphite pH 5.0 and DNA protection buffer (EpiTect Bisulfite Kit, Qiagen). The reaction mixture was incubated for four cycles of 5 min at 70°C followed by 1 h at 60°C and then desalted with Micro Bio‐spin 6 chromatography columns (Bio‐Rad). RNA was desulphonated by adding an equal volume of 1 M Tris (pH 9.0) to the reaction mixture and incubated for 1 h at 37°C, followed by ethanol precipitation. 120 ng of bisulphite‐converted RNA was used to generate Bisulfite‐seq libraries. Bs‐Seq libraries were performed according to TruSeq Small RNA preparation kit (Illumina). First 2′,3′‐cyclic phosphate and 5′‐hydroxyl termini produced during the bisulphite/desulphonation reaction were end‐repaired with T4 PNK and Spermidine (New England Biolabs). RNA adapters suitable for Illumina sequencing were then ligated, reverse‐transcribed at 50°C for 1 h with SuperScript III and 1 mM of each dNTP (SuperScript III cDNA synthesis kit, Invitrogen) followed by 18‐cycle PCR amplification. The amplified product was not size‐selected before sequencing.
Small RNA Illumina library preparation protocols were used for both tRNA-seq and Bisulphite-seq.


title: Ribosome profile NSun2 -/- 1


title: kin28as_1napp1-rep1

description: 2 uM


title: Ribosome profile WT1


title: Adult_cre_negative_rep2

description: Ribosome-bound mRNAs

value: Adult


title: kin28is_dmso-rep1

description: 2 uM


title: RNA Bisulphite sequencing NSun2 -/- 3


title: kin28as_dmso-rep1

description: 2 uM


title: Adult_retina_rep2

description: Ribosome-bound mRNAs


title: PE8 HELP-tagging

description:
HpaII test for HELP-tagging
JG30


title: PE7 HELP-tagging

description:
HpaII test for HELP-tagging
JG29


title: Adult_retina_rep1

description: Ribosome-bound mRNAs


title: PE6 HELP-tagging

description:
HpaII test for HELP-tagging
JG28


title: WT_cmk-rep1

description: 2 uM


title: Hypertension2 HELP-tagging

description:
HpaII test for HELP-tagging
JG26


title: PE9 HELP-tagging

description:
HpaII test for HELP-tagging
JG31


title: Adult_cre_negative_rep1

description: Ribosome-bound mRNAs


title: Hypertension3 HELP-tagging

description:
HpaII test for HELP-tagging
JG27


title: RNA Bisulphite sequencing NSun2 -/- 1


title: Adult_cre_positive_rep2

description: Ribosome-bound mRNAs


title: Adult_cre_positive_rep1

description: Ribosome-bound mRNAs


title: RNA Bisulphite sequencing NSun2 -/- 2


title: WT_1napp1-rep1

description: 2 uM


title: Cont7 HELP-tagging

description:
HpaII test for HELP-tagging
JG25


title: RNA Bisulphite sequencing WT4


title: P7_retina_rep2

description: Ribosome-bound mRNAs


title: tRNA NSun2 -/- 4

description: transfer RNA


title: RNA Bisulphite sequencing WT1


title: tRNA NSun2 -/- 2

description: transfer RNA


title: RNA Bisulphite sequencing WT3


title: P7_cre_negative_rep2

description: Ribosome-bound mRNAs


title: P1_retina_rep2

description: Ribosome-bound mRNAs


title: Cont6 HELP-tagging

description:
HpaII test for HELP-tagging
JG21


title: PE4 HELP-tagging

description:
HpaII test for HELP-tagging
JG20


title: P7_cre_positive_rep2

description: Ribosome-bound mRNAs


title: PE5 HELP-tagging

description:
HpaII test for HELP-tagging
JG23


title: Hypertension1 HELP-tagging

description:
HpaII test for HELP-tagging
JG17


title: tRNA NSun2 -/- 1

description: transfer RNA


title: P7_cre_negative_rep1

description: Ribosome-bound mRNAs


title: tRNA NSun2 -/- 3

description: transfer RNA


title: P7_cre_positive_rep1

description: Ribosome-bound mRNAs


title: Cont5 HELP-tagging

description:
HpaII test for HELP-tagging
JG12


title: WT_dmso-rep1

description: 2 uM


title: PE2 HELP-tagging

description:
HpaII test for HELP-tagging
JG18


title: P1_cre_negative_rep2

description: Ribosome-bound mRNAs


title: PE3 HELP-tagging

description:
HpaII test for HELP-tagging
JG19


title: Cont3 HELP-tagging

description:
HpaII test for HELP-tagging
JG06


title: Cont4 HELP-tagging

description:
HpaII test for HELP-tagging
JG08


title: RNA Bisulphite sequencing WT2


title: tRNA WT4

description: transfer RNA


title: P7_retina_rep1

description: Ribosome-bound mRNAs


title: Cont1 HELP-tagging

description:
HpaII test for HELP-tagging
JG04


title: P1_cre_positive_rep2

description: Ribosome-bound mRNAs


title: P1_retina_rep1

description: Ribosome-bound mRNAs


title: tRNA WT2

description: transfer RNA


title: Cont2 HELP-tagging

description:
HpaII test for HELP-tagging
JG05


title: 4C-Seq for shox promoter in human U2OS cells

city: Seville

first: Ana

last: Fernandez-Miñan

address: Crta. Utrera, km.1

country: Spain

institute: CABD-CSIC-UPO

data_processing:
library strategy: 4C-Seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Chicken May 2006 assembly (galGal3) or Human February 2009 (hg19) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Raw reads were converted into reads/1kb bin, and a running 5 bins-window smoothing algorithm was used to smooth the data.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: galGal3/hg19
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 2Mb around each viewpoint that can be directly uploaded to UCSC for visualization.

source_name: U2OS human cells

growth_protocol: Cells are grown in a 37ºC incubator at 5% CO2.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

treatment_protocol: No treatment

value: osteosarcoma cell line U2OS


title: E17_cre_negative_rep2

description: Ribosome-bound mRNAs


title: P1_cre_negative_rep1

description: Ribosome-bound mRNAs


title: tRNA WT3

description: transfer RNA


title: Induced spermatocytes replicate1

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
RNA-seq reads generated from each sample were aligned to the mouse genome (UCSC mm9) with Tophat-2.0.6.
Mapped reads were subsequently assembled into transcripts guided by reference annotation (mm9, USCS gene annotation) with Cufflink-2.0.2.
Differential gene and expression analysis was conducted by using cuffdiff.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: bigWig files were generated using bam2wig; The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. Excel files contain FPKM values.

source_name: Induced spermatocytes

extract_protocol:
Total RNAs were isolated with TRIZOL (Invitrogen) reagent and purified with RNase-free DNase I to remove contaminated DNA if any. Then the RNA samples were subjected to RNA sequencing following manufacturer’s recommendations (Novogene) using Illumina Hiseq 2000 instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: mSSCs were cultured on laminin-coated dishes overnight and then treated with vehicle, 100 nM RA, and 100 nM RA plus 0.25 mg/ml cycloheximide for 24 h, respectively. For RNA sequencing of induced germ cells, GFP-mSSCs were cultured on mitomycin-inactivated pup Sertoli cells and induced for different days. After a 3-day induction, GFP- and c-KIT-positive differentiating spermatogonia (idSG) were collected by FACS. Induced spermatocytes (iSC) were collected after a 6-day induction by sorting the GFP-positive and c-KIT-negative cell population.

value: DBA/C57 F1

tag: tissue

value: testis

value: male

value: wild type


title: E17_cre_positive_rep2

description: Ribosome-bound mRNAs


title: T0 - untrained horses_4

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Equus caballus genome (EquCab2.0) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Genome_build: EquCab2.0
Supplementary_files_format_and_content: raw.gene.csv.gz: compressed gzip file containing raw genes counts
Supplementary_files_format_and_content: genes_AB.csv.gz: compressed gzip file containing raw counts (T1 vs T2) for genes
Supplementary_files_format_and_content: genes_BC.csv.gz: compressed gzip file containing raw counts (T2 vs T3) for genes
Supplementary_files_format_and_content: genes_CD.csv.gz: compressed gzip file containing raw counts (T3 vs T0) for genes

organism: Equus caballus

extract_protocol:
From horses at the different training periods, the blood samples were collected from the jugular vein into Tempus™ Blood RNA Tube (Ambion, Life Technologies) and stored at -20°C. Total RNA was isolated using by MagMAX™-96 Total RNA Isolation Kit (Ambion, Life Technologies) according to manufactured protocol. The quality and quantity of obtained RNA samples were checked using by NanoDrop 2000 (ThermoScientific) and TapeStation 2200 instrument with Agilent RNA ScreenTape (Agilent, Perlan Technologies).
The cDNA libraries were prepared from 400ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.

value: blood

value: 2.5 year old

tag: breed

value: Arabian

value: female


title: T0 - untrained horses_6


title: Induced differentiating spermatogonia replicate2

source_name: Induced differentiating spermatogonia


title: T0 - untrained horses_5


title: T0 - untrained horses_3


title: P1_cre_positive_rep1

city: Cambridge

description: Ribosome-bound mRNAs


title: T0 - untrained horses_2

value: 3 year old


title: E17_retina_rep1

description: Ribosome-bound mRNAs


title: E17_cre_negative_rep1

description: Ribosome-bound mRNAs


title: tRNA WT1

description: transfer RNA


title: E17_cre_positive_rep1

description: Ribosome-bound mRNAs


title: mouse striatum_p0_mutant_Drd2-Cre;Sp9Flox/Flox_rep2

first: Zhengang

last: Yang

address: 138 Yi Xue Yuan Road

department: Institutes of Brain Science and State Key Laboratory of Medical Neurobiology

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:GRCm38.p4）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: striatum

extract_protocol:
Total RNA was extracted using mir VanaTM miRNA Isolation kit (Cat#AM1561, Ambion) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The striatum (including SVZ) from P0 littermate controls and Sp9 conditional mutants were dissected.These tissues were then put into -80 oC

value: a mixed genetic background of C57BL/6J, 129S6 and CD1

value: striatum

value: post natal day 0


title: PE1 HELP-tagging

description:
HpaII test for HELP-tagging
JG01

value: Preeclampsia

value: Male

value: Amnion


title: T3 - horses and at the end of the racing season  (October)_7


title: mSSC replicate 1

source_name: mSSC


title: Induced spermatocytes replicate2


title: E17_retina_rep2

description: Ribosome-bound mRNAs


title: mSSC treated with RA and CHX replicate2

source_name: mSSC treated with RA and CHX


title: mouse striatum_p0_mutant_Drd2-Cre;Sp9Flox/Flox_rep3


title: mouse striatum_p0_control_Sp9Flox/Flox_rep1


title: T3 - horses and at the end of the racing season  (October)_8


title: T3 - horses and at the end of the racing season  (October)_4


title: Induced differentiating spermatogonia replicate1


title: mouse striatum_p0_control_Sp9Flox/Flox_rep2


title: T3 - horses and at the end of the racing season  (October)_5


title: mouse striatum_p0_control_Sp9Flox/Flox_rep3


title: mSSC replicate 2


title: mSSC treated with RA replicate2

source_name: mSSC treated with RA


title: mSSC treated with RA and CHX replicate1


title: T3 - horses and at the end of the racing season  (October)_1


title: d2_wt_4

city: New York

first: Jane

last: Skok

address: 550 First Ave, Smillow 307

institute: NYU

description: replicate 4

data_processing:
Library strategy: 4C-Seq
The first 4 nucleotides in each read (corresponding to barcode) and the nucleotides corresponding to the DpnII primer ( TCTGTCCTAAAGGCTCTGAGATC) were trimmed from the 5' of the read
Mapping was performed using Bowtie2 to a reduced genome consisting of all unique 24 nucleotide-long regions surrounding DpnII sites allowing for zero mismatches.
Analysis of 4C-Seq signal was performed by building successive 10kb windows with 95% overlap and calculating the total number of reads per window. The following mm10 coordinates were used for this analysis Chr12: 113175000-113475000.
For comparison between genotypes and/or conditions DESeq2 1.10.0 with default parameters was used to normalize total read count per window between samples
Genome_build: mm10
Supplementary_files_format_and_content: bedGRaph - normalized 4C signal for 10 kb windows in the region surrounding the Igh locus

source_name: Activated B cells

growth_protocol: Mice from C57BL/6 were used to isolate splenic lymphocytes. Naïve B cells were isolated using  aCD43 depletion

extract_protocol:
4C-Seq was prepared using DpnII and Csp6 digestions.
Library was prepared by PCR using the following primers: TCTGTCCTAAAGGCTCTGAGATC and GAACACAGAAGTATGTGTATGGA

treatment_protocol: B cells were plated at 0.25x106 cells/ml in RPMI 10% FCS and activated with 5ng/ml of IL4 (Sigma) and 1µg/ml of αCD40 (Bioexcell).

value: Wild-type

value: Activated B cells


title: T3 - horses and at the end of the racing season  (October)_3


title: mSSC treated with vehicle replicate1

source_name: mSSC treated with vehicle

value: DBA/C57 F1


title: mSSC treated with vehicle replicate2

value: testis


title: T3 - horses and at the end of the racing season  (October)_2

value: male


title: mSSC treated with RA replicate1

value: wild type


title: d2_wt_3

description: replicate 3


title: mouse striatum_p0_mutant_Drd2-Cre;Sp9Flox/Flox_rep1


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_10

value: blood


title: d2_dko_1

description: replicate 1


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_9


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_11


title: d2_wt_2

description: replicate 2


title: d2_wt_1

description: replicate 1


title: T3 - horses and at the end of the racing season  (October)_6


title: d2_53bp1_3

description: replicate 3


title: d2_dko_2

description: replicate 2


title: d2_53bp1_2

description: replicate 2


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_7


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_6


title: d2_dko_3

description: replicate 3


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_5


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_3


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_4


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_2


title: d0_wt_3

description: replicate 3

source_name: Resting B cells

value: Resting B cells


title: dermal beta-catenin Mutant3

city: Cleveland

first: Radhika

middle: Paresh

last: Atit

state: Ohio

address: 2074 Adelbert Road, Millis 316

institute: Case Western Reserve University

data_processing:
Sequencing was carried out on the Illumina HiSeq 2500 platform. Resulting 50-base single-end reads were mapped to mouse genome release mm10.
Alignment of paired-end reads to mm10 was performed using GSNAP, with 2 mismatches allowed for the full length of the reads.
Mapped unique raw reads that mapped to genes in the RefSeq database were counted using HTSeq and normalized to the total of mapped reads in each condition.
Differential gene expression analysis was performed using TopHat and Cuff diff.  Genes were considered statistically significant if they had p-values less than 0.05 after adjusting for false discovery rate with the Benjamini and Hochberg method {Benjamini:1995ws} in a negative binomial test and showed 1.5 fold-changes between compared conditions.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values

extract_protocol:
Dermal fibroblast progenitors were FACS sorted and stored in Trizol.  Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 200-400ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: EnlCre/+;RRYFP;Bcatflox/null

value: CD1/ C57Bl6


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_1

value: 3 year old

value: Arabian

value: female


title: d2_53bp1_1

description: replicate 1


title: dermal beta-catenin Mutant1


title: T0 - untrained horses_1

value: 2.5 year old


title: T2 - horses before racing season and after intense gallop phase - trained horses (May)_8


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_12


title: 4C-Seq for shox promoter in limbs from HH28 chicken embryos

organism: Gallus gallus

source_name: HH28 chicken embryos

growth_protocol: Embryos raised at 38ºC until HH28

tag: developmental stage

value: Hamburger and Hamilton stage (HH) 28 embryo

value: limbs


title: Control2

value: En1Cre/+; RRYFP/+


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_10


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_9


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_5


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_11


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_2


title: Control1


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_8


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_6


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_7


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_1


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_4


title: T1 - horses at intensive training stage (after the slow canter phase) (March)_3


title: LRSKBr3_ERRaChIP_Replicate1

status: Public on Jun 15 2016

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

description:
G31
Replicate of G34
processed data file: LRSKBr3(G31_G34_(G36))_ERRChIP_peaks.bed

data_processing:
Reads were filtered for quality (phred33 score >= 30) and length (n >= 32) trimming using FASTX Toolkit 0.0.13.1
Filtered reads were aligned to the reference assembly hg19 using bwa v0.5.9. Only uniquely mapped reads were retained for further analysis. Redundant reads were removed using SAMtools v0.1.18
Peaks were called using MACS1.4.1 with default values (mfold [10,30], p-value 1e-05)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated using MACS1.4.1 (default parameters). Bed files contain peak calls on merged reads using corresponding inputs as control. Scores represent peak intensity.

source_name: LRSKBr3 cells lapatinib-resistant cells

growth_protocol: Cells (SKBr3 or BT-474) were cultured in DMEM supplemented with 10% FBS. Lapatinib-resistant SKBr3 cells were maintained in 2 uM lapatinib.

extract_protocol:
Lysates were extracted from sonicated 1% formaldehyde-crosslinked nuclei and histone-DNA complexes were isolated with ERRalpha antibody. DNA was purified using QIAquick PCR Purification Kit. Libraries were prepared using the Illumina TruSeq ChIP Library Prep Kit
Libraries were prepared at McGill University and Génome Québec Innovation Centre according to the Illumina TruSeq ChIP Library Prep Kit

treatment_protocol: For EGF/Heregulin treatment, cells were serum-starved for 24h and treated with 100 uM EGF/heregulin or vehicle prior to harvesting.

tag: treatment

value: lapatinib 2uM

tag: factor chip

value: ERRalpha

tag: tissue of origin

value: breast


title: LRSKBr3_ERRaChIP_Replicate2

description:
G34
Replicate of G31
processed data file: LRSKBr3(G31_G34_(G36))_ERRChIP_peaks.bed


title: pSKBr3_ERRaChIP_Replicate2

description:
G32
Replicate of G29
processed data file: pSKBr3(G29_G32_(G35)_ERRChIP_peaks.bed

source_name: pSKBr3 cells parental sensitive

value: untreated


title: pSKBr3_Input

description:
G35
Input for G29 and G32
processed data file: pSKBr3(G29_G32_(G35)_ERRChIP_peaks.bed

value: input


title: WT_BMDMs_T0_2

city: Boston

first: Ramnik

middle: J

last: Xavier

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description:
N704_B1
Stranded 3' digital gene expression
i7index1: TCCTGAGC
Barcode: CCGTAT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to mouse genome (mm10) using BWA-0.7.4 which uses the Burrows-Wheeler transform as described by Li H. and Durbin R. (Bioinformatics 2009, 25:1754-60.)
RSEM-based quantification using known transcripts was performed using protocol described by Li et al (BMC Bioinformatics 2011, 12:323)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files contain matrix of UMI counts

source_name: mouse cultured BMDMs (primary cells in culture)

growth_protocol: Cell were cultured in RPMI with 10% heat-inactivated FBS with pen-strep and 20ng/ml recombinant murine MCSF

extract_protocol:
Cells were washed in 1X PBS and lysed directly in Ambion mRNA direct lysis buffer.
RNA libraries were prepared as described in http://biorxiv.org/content/early/2014/03/05/003236

treatment_protocol: BMDMs were cultured for seven days and then harvested for RNA isolation

tag: gender

tag: chimera genotype

value: chimera WT--> WT

value: bone marrow chimera

value: macrophage

tag: age

value: 8 weeks old


title: GPR65KO_BMDMs_T0_1

description:
N705_D1
Stranded 3' digital gene expression
i7index1: GGACTCCT
Barcode: AAGCTG

value: chimera GPR65KO--> WT


title: WT_BMDMs_T0_1

description:
N704_A1
Stranded 3' digital gene expression
i7index1: TCCTGAGC
Barcode: AAGCTG


title: GPR65KO_BMDMs_T0_3

description:
N705_F1
Stranded 3' digital gene expression
i7index1: GGACTCCT
Barcode: GTAGTC


title: LRSKBr3_Input

description:
G36
Input for G31 and G34
processed data file: LRSKBr3(G31_G34_(G36))_ERRChIP_peaks.bed


title: d0_wt_2

description: replicate 2

value: Wild-type

value: Resting B cells


title: GPR65KO_BMDMs_T0_2

description:
N705_E1
Stranded 3' digital gene expression
i7index1: GGACTCCT
Barcode: CCGTAT

value: female


title: d0_wt_1

description: replicate 1


title: BT-474_HRG_ERRaChIP

description:
G27
G28 is the input
processed data file: BT474_hrg_G27_peaks.bed

source_name: BT-474 cells

value: starved, 100uM HRG 90min


title: BT-474_nt_Input

description:
G28
Input for G25, G26, G27

value: starved, PBS


title: pSKBr3_ERRaChIP_Replicate1

description:
G29
Replicate of G32
processed data file: pSKBr3(G29_G32_(G35)_ERRChIP_peaks.bed


title: BT-474_EGF_ERRaChIP

description:
G26
G28 is the input
processed data file: BT474_egf_G26_peaks.bed

value: starved, 100uM EGF 90min


title: SKBr3_EGF_Input

description:
G2
Input for G6 and G23
processed data file: SKBr3_EGF_(G6_G23_(G2))_ERRChIP_peaks.bed

source_name: SKBr3 cells


title: SKBr3_Hrg_Input

description:
G3
Input for G8 and G24
processed data file: SKBr3_hrg_(G8_G24_(G3))_ERRChIP_peaks.bed


title: SKBr3_EGF_ERRaChIP_Replicate2

description:
G23
Replicate of G6
processed data file: SKBr3_EGF_(G6_G23_(G2))_ERRChIP_peaks.bed


title: dermal beta-catenin Mutant2

value: skin

value: EnlCre/+;RRYFP;Bcatflox/null

value: CD1/ C57Bl6


title: SKBr3_nt_ERRaChIP_Replicate1

description:
G4
Replicate of G22
processed data file: SKBr3_nt_(G4_G22_(G1))_ERRChIP_peaks.bed

value: ERRalpha

value: breast


title: BT-474_nt_ERRaChIP

description:
G25
G28 is the input
processed data file: BT474_nt_G25_peaks.bed


title: SKBr3_Hrg_ERRaChIP_Replicate1

description:
G8
Replicate of G24
processed data file: SKBr3_hrg_(G8_G24_(G3))_ERRChIP_peaks.bed


title: SKBr3_Hrg_ERRaChIP_Replicate2

description:
G24
Replicate of G8
processed data file: SKBr3_hrg_(G8_G24_(G3))_ERRChIP_peaks.bed


title: SKBr3_nt_ERRaChIP_Replicate2

description:
G22
Replicate of G4
processed data file: SKBr3_nt_(G4_G22_(G1))_ERRChIP_peaks.bed


title: SKBr3_nt_Input

description:
G1
Input for G22 and G4
processed data file: SKBr3_nt_(G4_G22_(G1))_ERRChIP_peaks.bed

value: input


title: ANK1_B4_2_1_CMK_I1

city: Rehovot

first: Omer

last: Schwartzman

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

data_processing:
The data was processed using our UMI-4C pipeline. With default parameters.
Processed reads were mapped with bowtie2 with the parameters:  --reorder --end-to-end.
Genome_build: hg19
Supplementary_files_format_and_content: The processed adj files are a 3 columns tab delimited table with headers: fragment end id1 (fend1), fragment end id2 (fend2), UMI count (count)

source_name: CMK cells

growth_protocol: Human leukemia cell lines, CMK, CMY, CHRF, and K562 were grown in RPMI (GIBCO) supplemented with 10% FBS, 1% glutamine (GIBCO), penicillin (100 U/mL), and streptomycin (100 μg/mL). Wi38 cells were grown in DMEM supplemented with 10% FBS, 1 mM sodium pyruvate, 1% glutamine (GIBCO), penicillin (100 U/mL), and streptomycin (100 μg/mL). (GIBCO) All cell lines were grown at 37°C and 5% CO2.

extract_protocol:
10^7 cells used to generate the primary 3C template. Cells are collected, centrifuged at 1200rpm, the supernatant is removed and are resuspended in PBS/10% FBS. Then the cells are cross-linked with formaldehyde to final concentration of 2% for 10min. The reaction is quenched by addition of glycine to final concentration of 0.125M. The cells are then centrifuged and resuspended in cold lysis buffer (50 mM Tris–HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100, 1 tbl Protease inhibitor). The nuclei are extracted and resuspended in 450µl UPW. For digestion, we add 60µl DpnII buffer, 15µl 10% SDS and incubate on a Thermomixer (Eppendorf) 37c, 60 minutes. 75µl of 20% TX-100 are added and the tube is incubated again 37c, 60 minutes. The chromatin is then digested with HC DpnII (NEB R0543M) in three rounds as following: 200U for 2 hours, 200U overnight and 200U for 2 hours. An aliquot is taken from the tube and run on gel to inspect digestion efficiency. The enzyme is then inactivated by incubating 65c, 20min. Next, the chromatin is ligated with 15µl of HC T4 ligase (NEB M0202M), with 10x ligase buffer to final volume of 7mL and incubated overnight at 16c. Aliquot is taken from the sample and ran on gel to inspect ligation efficiency. The chromatin is then reverse cross-linked overnight at 65c with 30ul proteinase K (Sigma-Aldrich), and then 30ul  of RNase A are added and incubated for 45 minutes, 37c. The 3C DNA is then extracted with Phenol-Chloroform resuspended in 10mM Tris-Hcl pH 8 and stored in -20c.
5-10ug DNA in 200µl Elution Buffter (EB, 10mM Tris-HCl, pH 8) of 3C template is sonicated at 4°c using Bioruptor program: 5 cycles of 30s on, 60s off. The sonicated material is inspected by running 10µl on agarose gel to assure size distribution of 450-550 bps. The sonicated DNA is subjected to end-repair reaction - 20µl 10X end-repair buffer and 10µl end-repair mix (NEB E6050L) are added to the mix and incubated at 20°c for 30 minutes. The DNA is cleaned by x2.2 AmpureXP beads (Beckman Coulter) and eluted in 76µl EB. Two nested PCR reactions are used for UMI-4C library construction. The PCR reactions are performed in 50ul volume with the following reagents: 10ul GoTaq Flexi buffer (promga M792A), 3ul MgCl 25mM (promega A3511), 0.2mM dNTPs, 2µl 10mM bait primer (0.4mM final concentration), 2µl 10mM Illumina enrichment primer 2 (0.4mM final concentration), 1ul GoTaq (promga M3008) and 200ng UMI-4C DNA template. PCR program is 2 minutes 95°c, 20 cycles of 30s 95°c, 30s 56°c, 60s 72°c, final extension of 5min 72°c. Following the PCR reaction we clean the amplified DNA with x1 SPRI beads and use 75% of the eluate to a second PCR reaction. The second PCR reaction is identical to the first. The only difference is the use of the bait primer with the Illumina dangling adapter (As shown in figure 1B). In the second PCR reaction 15-18 cycles are used instead of 20. Then, A-tailing reaction is performed with 10µl NEBbuffer2, 4µl Klenow (NEB M0212M), and 10µl 10nM dATP. Following A-tailing, the 5’ ends of the DNA are dephosphorylated with 2µl of Alkaline Phosphatase (NEB M0290S) 50°c for 60 minutes, and the DNA is cleaned with AmpureXP beads (x2) and eluted in 67µl EB. The DNA template is ligated with 5µl 15µM Illumina indexed adapters (final concentration 0.4µM), 10µl ligase mix and 80µl 10X buffer (NEB M2200). To release the non-ligated strand of the adapter, the DNA is denatured at 95°c for 2 minutes and cleaned with SPRI beads x1.

value: Mega-Erythroleukemia

tag: linage

value: Hematopoietic

tag: viewpoint


title: G1_3_5kb_B3_1_1_k562_I2

source_name: K-562 cells


title: G1_3_5kb_B3_1_1_CMK_I1


title: SKBr3_EGF_ERRaChIP_Replicate1

description:
G6
Replicate of G23
processed data file: SKBr3_EGF_(G6_G23_(G2))_ERRChIP_peaks.bed


title: G1_3_5kb_B3_1_1_k562_I1


title: G1_3_5kb_B3_1_1_CMY_I2

source_name: CMY cells


title: G1_3_5kb_B3_1_1_CMY_I1


title: G1_3_5kb_B3_1_1_CMK_I2


title: ANK1_B4_2_1_k562_I1


title: G1_165kb_B2_1_1_DND41_I1_HS

description:
The processed data file contains reads from two separate runs which were concatenated.
adj.G1_165kb_2_1_1.DND41_I1

source_name: DND41 cells

value: Lymphoblastic leukemia


title: G1_3_5kb_B3_1_1_Chrf_I1

source_name: CHRF cells


title: G1_165kb_B2_1_1_CMK_I2_HS

description:
The processed data file contains reads from two separate runs which were concatenated.
adj.G1_165kb_2_1_1.CMK_I2


title: G1_165kb_B2_1_1_CMK_I1_HS

description:
The processed data file contains reads from two separate runs which were concatenated.
adj.G1_165kb_2_1_1.CMK_I1


title: G1_50kb_B2_1_1_DND41_I1


title: G1_165kb_B2_1_1_k562_I1_HS

description:
The processed data file contains reads from two separate runs which were concatenated.
adj.G1_165kb_2_1_1.k562_I1


title: ANK1_B4_2_1_DND41_I1


title: G1_50kb_B2_1_1_DND41_I2


title: G1_50kb_B2_1_1_k562_I2


title: G1_50kb_B2_1_1_k562_I1


title: G1_50kb_B2_1_1_CMK_I2


title: G1_50kb_B2_1_1_CMK_I1


title: G1p1_B2_1_1_k562_I2


title: G1_3_5kb_B3_1_1_DND41_I1


title: G1_3_5kb_B3_1_1_Chrf_I2


title: G1p1_B2_1_1_k562_I1


title: G1_165kb_B2_1_1_DND41_I2_HS

description:
The processed data file contains reads from two separate runs which were concatenated.
adj.G1_165kb_2_1_1.DND41_I2


title: G1_165kb_B2_1_1_k562_I2_HS

description:
The processed data file contains reads from two separate runs which were concatenated.
adj.G1_165kb_2_1_1.k562_I2


title: G1p1_B2_1_1_DND41_I1


title: G1p1_B2_1_1_CMY_I2


title: G1p1_B1_2_1_k562_I1


title: G1p1_B2_1_1_CMY_I1


title: G1p1_B2_1_1_Chrf_I2


title: G1p1_B1_2_1_DND41_I1


title: G1p1_B2_1_1_Chrf_I1


title: G1p1_B2_1_1_CMK_I1


title: G1p1_B1_2_1_CMK_I2


title: G1p1_B1_2_1_CMY_I1


title: G1p1_B1_2_1_CMK_I1


title: A431 110k rep2 (EV)

city: Montreal

first: Fabio

middle: Alexis

last: Lefebvre

state: Quebec

address: 110 Ave des Pins

department: RNA biolog

institute: IRCM

data_processing:
Read quality was confirmed using FastQC v0.10.1 and trimming was performed with Trimmomatic when deemed necessary.
Read alignment was performed using Tophat v2.0.10 on the human GRCh37/hg19 and the Drosophila BDGP5.78/dm3 genomes, respectively.
Ribosomal RNA sequences were filtered out by first mapping the reads to FASTA files of genes annotated as rRNA in Ensembl.  Remaining reads were then re-aligned to reference genomes with Tophat.
BAM files were used for expression analyses with Cuffdiff v2.2.1 without effective length correction.
Genome_build: GRCh37/hg19 (human) and BDGP5.78/dm3 (Drosophila)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: A431 EV

growth_protocol: Human HepG2 and A431 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 1% of a 1:100 solution of penicillin and streptomycin (pen/strep) and 10% fetal bovine serum (depleted FBS) (Wisent). Before use, FBS was depleted of bovine EVs by ultracentrifugation (110,000 g, 18h, 4°C). Human cells were cultured at 37 °C, in an atmosphere of 5% CO2 in T-flasks of 175 cm2 and routinely detached using 0.25% trypsin upon reaching 80% confluence. Drosophila D17 and S2R+ cells were respectively maintained in Shield and Sang Insect Medium (M3) and in Schneider medium. Both media were supplemented with 1% of a 1:100 pen/strep solution and 10% depleted FBS. M3 medium additionally contained insulin (20 μg/mL). Droso¬phila cells were cultured at 25°C.

extract_protocol:
EVs and corresponding cellular pellets were resuspended in 1 mL of TRIzolTM reagent (Ambion) and processed according to the manufacturer's instructions RNA extracts were purified with the RNA Clean & ConcentratorTM-5 system (Zymo Research).  In-column DNase I (New England BioLabs) treatment, RNA washes and elution steps were performed according to the manufacturer's instructions. One additional centrifugation step was included (5 min at 16,000×g) to ensure complete removal of the washing buffer.  RNA samples were eluded in 12 μL of RNAse-free water (Wisent). Absorbance distributions were immediately quantified using a NanoDrop 2000c spectrophotometer.  RNA samples were  pure ( A260/A280 ≥ 2.0)( 2.00 ≤ A260/A230 ≤ 2.25). Aliquots of ~5 ng were submitted to capillary electrophoresis on a Bioanalyzer 2100 machine (Agilent). RNAse protection assay was performed to confirm the intraluminal topology of exRNA within EVs.  D17 and HepG2 cellular RNA extracts were used as controls. RNAse A (Qiagen) was inactivated by heat (10 min at 65 ºC) and RNA was extracted as described above.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For EV isolation, cells were kept at low passage (P<10) and cultured for approximately 48h starting from ~10^7 cells.  EVs were isolated according to an established differential ultracentrifugation protocol (Thery, C., et al. Curr Protoc Cell Biol, 2006. ). Briefly, fresh culture supernatants (~80 mL) were cleared of floating (10 min at 400×g) and dead cells (10 min at 2000×g) using a 5810 R centrifuge (Eppendorf). Cell debris were removed (30 min at 10,000×g) and EVs were pelleted (70 min at 110,000×g) using the Sw28 and the Sw32 Ti rotor (Beckman Coulter) in an L8-70M machine (Beckmann). Preparations were extensively washed with PBS and pelleted (70 min at 110,000×g) using a RP100-AT4 rotor (Sorvall) and a RC-M100 micro ultracentrifuge (Sorvall). All steps were performed at 4 °C and EVs were immediately processed for analysis.

value: A431 squamous cell carcinoma cell line

tag: cell passages

tag: rna source

value: EV


title: HepG2 110k rep1 (EV)

source_name: HepG2 EV

value: HepG2 hepatocellular carcinoma cell line


title: HepG2 110k rep2  (EV)


title: HepG2 total cellular rep1

source_name: HepG2 total cellular

value: total cellular RNA


title: rip_RocA03 [Sample 19]

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
For Ribosome profiling, mRNA-Seq, and RIP-Seq:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
Read quantitation using custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (amino acid) used for read counting;3. read counts
For Bind-n-Seq:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Depleting duplicated reads with Fast-X-toolkit
Supplementary_files_format_and_content: The fasta file was made by FASTX-Tool kit FASTA/Q Collapser, to eliminate duplicated sequence. Sequence is named with two number, a running number followed by how many  times that sequence occurred.

source_name: HEK 293 T-Rex_rip_RocA03

extract_protocol:
Standard mRNA-seq
TRI-reagent (sigma) and following Direct-zol RNA-MiniPrep (zymo research).

value: HEK 293 T-REx cell

value: stabley expressing SBP-tagged eIF4A

value: RocA 0.3 uM

tag: molecule

value: total RNA