title: CHiC-Inv1-ESC

city: Berlin

first: Andreas

last: Magg

state: Berlin

address: Ihnestraße 63-73

department: Development and Disease

country: Germany

institute: Max-Planck-Institute for Molecular Genetics

data_processing:
Library strategy: Capture Hi-C-seq
Preprocessing and mapping of paired-end raw sequencing reads, as well as filtering of mapped di-tags was performed with the Hi-CUP pipeline v.0.5.8 (Wingett et al., 2015) (Nofill: 1, no size selection, Format: Sanger). The pipeline uses the alignment tool bowtie2 v.2.2.6 (Langmead and Salzberg, 2012) for mapping short reads to the reference genome (mm9). Aligned and filtered reads were combined for all replicates and further reduced to a minimum mapping quality of MAPQ=30. Filtered di-tags were further processed with the Juicer tool kit (Durand et al., 2016) (v1.7.5) to bin di-tags (10 kb bins) and to normalize the interaction matrix by the Knight-Ruiz (KR) matrix balancing method (Durand et al., 2016; Knight and Ruiz, 2013; Lieberman-Aiden et al., 2009). The DNA-capturing step enriches the genomic region chr1:71,000,001-81,000,000 on mm9 leading to three different regimes in the cHi-C map: (i) enriched versus enriched, (ii) enriched versus non-enriched, and (iii) non-enriched versus non- enriched. For binning and normalization only di-tags in regime (i) were considered.
All maps were mapped to a customized reference genome that incorporates the respective inversion. Additionally the capture-Hi-C map that is based on the WT experiment was also mapped to each customized reference genome and interaction matrices were generated. Half of this map was subsequently substracted from all heterozygous contact matrices to generate a homozygous map that is just showing the inversion. For this the WT map and the respective heterozygous map were scaled to the same amount of reads. For the substraction of interaction maps all maps were converted to reads per million (RPM) to account for different sequencing depths.
Genome_build: mm9
Supplementary_files_format_and_content: txt (Pairwise interactions)

source_name: Embryonic Limb Bud

growth_protocol: Forelimb and hindlilmb buds were micro-dissected from E11.5 mouse embryos

extract_protocol:
Preparation and fixation of limb tissue and ESCs was performed according to the instructions of the Hi-C protocol. Fixed cell pellets were resuspended in cHi-C lysis buffer (final concentration of 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 M EGTA, and 1x Complete protease inhibitors (Roche)) and incubated on ice for 10 minutes. Lysis buffer was removed by centrifugation at 400 g for 5 minutes at 4°C, succeeding to removal of supernatant, snap-freezing and storage at -80°C. The following day, the thawed pellet was resuspended in 360 µl H2O, 60 µl 10x DpnII buffer and 15 µl 10% SDS. After 1 h of shaking with 900 rpm at 37°C 150 µl of 10% Triton-X-100 were added and the mixture incubated for another hour with the same conditions. 15 µl were taken as a control for undigested chromatin (stored at -20°C). Then, digestion of chromatin was initiated by adding 40 µl DpnII (10 U/µl, NEB R0543S) and incubated for 4 h at 37°C and shaking at 900 RPM. Chromatin was further digested by adding 30 µl DpnII and incubation of the sample overnight. The following day, another 30 µl DpnII were added and the samples shaken for 4 more hours. Inactivation of the enzyme was done by incubation at 65°C for 25 minutes. A 50 µl aliquot was taken to test digestion efficiency (stored at -20°C). Then, the library sample was transferred to a 50 ml falcon tube, diluted in 5.1 ml of water and mixed with 700 µl 10x T4-DNA-ligase buffer and 5 µl T4-DNA-ligase (30 U/µl, Thermo Fisher Scientific EL0013). After 4 hours of incubation in a 16°C water bath with manually shaking (once per hour) the sample was incubated for 30 min at RT. Through addition of 30 µl of Proteinase K, the samples were reverse-crosslinked overnight at 65°C. On the fourth day, RNA in the samples was digested by subjecting 30 µl of 10 mg/ml RNase, incubating 45 minutes at 37°C. Subsequent to addition of 7 ml phenol-chloroform, samples were centrifuged 15 min at 2440 g and RT. The water phase was transferred into a new tube and mixed with 7 ml H2O, 1 ml of 3 M sodium acetate (pH 5.6) and 35 ml of 100% ethanol. For precipitation of DNA, samples were kept overnight at -20°C and spun down with 5250 g for 45 min at 4°C. After a wash with 10 ml of 70% ethanol and 15 min of centrifugation (5250 g, 4°C), the pellet was air-dried and dissolved in 150 µl 10 mM Tris-HCl (pH 7.5). In order to check the 3C-library, 600 ng of chimeric DNA was loaded on a 1% gel together with the undigested and digested aliquots.
Next, the 3C-library was sheared using a Covaris sonicator with the conditions as for HiC (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 6 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C). After adaptors were added to the sheared DNA,  amplification was performed according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed sure-select probes and indexed for sequencing (50 to 100 bp paired-end) as instructed by Agilent protocols.

tag: genotype

value: mutant

tag: developmental stage

value: G4 ESC


title: 1001702104_O6

status: Public on Nov 19 2018

type: SRA

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

data_processing:
bcl2fastq demux
STAR mapping
Htseq-count 0.7+ gene counting
Stampy virus mapping
Custom script for filtering virus reads
Genome_build: grch38
Supplementary_files_format_and_content: One TSV for each sample containing the counts of gene expression.

molecule: total RNA

organism: Homo sapiens

source_name: blood (PBMCs)

extract_protocol:
No extraction, single cells are sorted into 0.4ul lysis buffer
Cells are lysed in lysis buffer containing Triton X-100, then RT using template switching oligo and preamplification for 21 cycles as in SmartSeq2 is performed. Cells with different levels of intracellular virus are cherry picked and sequencing libraries are made using illumina’s Nextera XT kit.

tag: tissue

value: blood

tag: patient id

tag: cell type

value: unknown

tag: Sex

value: F

tag: diseaseseverity

value: severe dengue

tag: numberhumanuniquelymappedreads

tag: numbervirusreads

tag: age


title: MEF_20

city: Hangzhou

first: Yishan

last: Chen

address: #866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
alignment was conducted with Tophat
The final gene expression data was normalized using Cuffnorm and represented as counts
Genome_build: mm9
Supplementary_files_format_and_content: Csv file includes raw counts of each gene from each sample

organism: Mus musculus

source_name: mouse embryonic fibroblasts

growth_protocol: Before treatment, MEFs were cultured in 10% FBS+ H-DMEM at a confluency of 90%. Mchons were cultured in 10% FBS + DMEM/F12 a confluency of 80-90%

extract_protocol: Single cells were lysated, preamplified and library prepared according C1-HT IFC protocol of Fluidigm Corporation.

treatment_protocol: Ci-Ics: MEFs treated by chemical cocktails (VCRTs) under hypoxia condition (5% O2) for 6 days. Ci-chons: chondrogensis induction of ci-Ics for 28 days.

tag: strain

value: embryonic fibroblasts

tag: passages

tag: treatment

value: growth medium

tag: time


title: MEF_19


title: MEF_18


title: CHiC-Inv1DelCTCF-Distal-E115

library_source: genomic

molecule: genomic DNA


title: 1001701101_A19

value: M

value: control


title: 1001701101_A20


title: 1001702104_O5


title: 1001702104_O4

value: monocyte


title: CHiC-Inv4-Distal-E115


title: 1001701101_A18

value: T cell


title: MEF_17


title: CHiC-Inv3-Distal-E115


title: 1001702104_O3


title: MEF_16


title: 1001701101_A17

value: NKT cell


title: 1001702104_O23


title: 1001701101_A16


title: CHiC-Inv2-Distal-E115


title: MEF_15


title: CHiC-Inv1-Distal-E115


title: 1001702104_O22


title: 1001702104_O8


title: CHiC-WT-Distal-E115

value: WT


title: MEF_14


title: 1001701101_A15


title: MEF_13


title: HiC_WT_E115-LB-Rep3

data_processing:
Raw reads were mapped to the mm9 genome using the Juicer pipeline (Durand et al. 2016, v1.5.6) which incorporates the alignment tool bwa (Li and Durbin 2009, v0.7.17). Merged mapped reads of all three replicates were subsequently filtered for a mapping quality >=30, summarized in 10kb windows and Knight-Ruiz (KR) normalized (Knight and Ruiz 2013) using the Juicer tool kit (Durand et al. 2016, v1.7.5). TAD domains were identified by applying TopDom (Shin et al. 2016, v0.0.2) using a 25kb window. For the detection of imbalanced structures between TAD boundaries HiC entries were further transformed into log2(observed/expected) (log2 O/E) using the Juicer tool kit to account for the exponential decay of the interaction signal. For this analysis just positive values are considered and a threshold for the upper quantile (98%) was applied to the data.
A training set consisting of high confident domains with balanced (negative set) and imbalanced (positive set) domain boundaries was hand-picked upon visual inspection on processed HiC matrices.  Based on log2 O/E transformed HiC matrices the location of the TAD boundaries were first improved by shifting the original boundary located at bin x to the bin ∈ [x-5, …, x, …, x+5] with the maximum mean signal. For all TADs, three imbalance measurements were calculated: the absolute difference of the averaged signals of the left and right anchored boundaries, the absolute log2 ratio of the averaged signals of both boundaries and the cosine similarity between the two boundaries. Whether the log2 ratio of the averaged signals is greater or lower zero gives the additional information about the position of the boundary anchor.  A random forest is grown for 100 trees using the training set and the three described imbalance measurements (using R package ‘randomForest’ v4.6-12). The trained model is then applied to all TAD domains whereas a domain is either classified as ‘imbalanced’ or ‘balanced’.  The domains are then ranked according to their imbalance probabilities (fraction of trees which voted for imbalanced structures between the boundaries) and the top 500 regions are further used for the analysis of enriched active enhancer regions at the TAD boundaries.
The top 500 imbalanced TAD boundaries were used and divided into left and right anchored stripes (according to the log2 ratio of the averaged boundary signals). Domains were divided into 100 bins and the fraction of each bin covering the Active 2 state  (which resembles active enhancers)  defined by EpicSeg segmentation was calculated. The results were additionally smoothed using LOESS regression (‘stat_smooth’ function in the ggplot2 R library, v2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: hic, bed

extract_protocol:
The HiC protocol was adapted from Rao et al., 2014. 3C-libraries were prepared from E11.5 limb buds as described previously (Hagege et al. 2007). HiC was performed as technical triplicates from limb buds of 8 embryos in total. After pooling the dissected tissue, it was turned into a single-cell suspension by digestion with Trypsin-EDTA 0.05% (Gibco) for 10 min at 37°C, disrupting the tissue by pipetting every 2 minutes. The cells were diluted in 10% FCS/PBS and homogenized using a 40 µm cell strainer (Falcon). Cells were pelleted by centrifugation (260 g, 5 minutes), resuspended in 10% FCS/PBS and fixed by adding 37% formaldehyde (Sigma-Aldrich) with a final concentration of 2% and put on a roller machine for 10 minutes at RT. By adding 1.425 M glycine (Merck) on ice,  fixation was quenched and the samples were immediately centrifuged at 260 g for 8 minutes. Supernatant was aspirated, the pellet resuspended in HiC lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1.15% Triton-X-100 and 1x Complete protease inhibitors (Roche)), incubated for 10 minutes on ice. Nuclei were pelleted, snap-frozen in liquid nitrogen and stored at -80°C. Frozen pellets were washed with 500 µl  DpnII buffer (NEB) and centrifuged for 5 minutes at 4°C. Then, the pellet was resuspended in 50 µl of 0.5% SDS, incubated for 10 minutes at 62°C, followed by addition of 145 µl of water, 25 µl of 10% Triton-X-100 (Sigma, 93443) and incubation at 37°C for 15 minutes. After taking a 15 µl aliquot as a control for undigested chromatin, 25 µl of 10x DpnII buffer and 10 µl of DpnII (100 U/µl; NEB) were added to the samples and chromatin was digested overnight at 37°C, rotating in an oven. The DpnII enzyme was inactived by incubation at 65°C for 25 minutes. An aliquot of 15 µl was taken to test digestion efficiency. Subsequent to pelleting the samples (5000 g, 5 minutes) and resuspending them in 200 µl of 1.2x NEBuffer 2, 50 µl of fill-in-mastermix (0.3 mM biotin-14-dATP (Life Technologies 19524-016), 0.3 mM dCTP, 0.3 mM dGTP, 0.3 mM dTTP, 0.8 U/µl DNA Polymerase I Large (Klenow), Fragment (NEB, M0210)) were added and samples were incubated at 37°C for 90 minutes with constant rotation in an oven. 900 µl of ligation-mastermix (1.33x NEB T4 DNA ligase buffer (NEB, B0202), 1% Triton-X-100, 0.13 mg/ml BSA, 2.2 U/µl T4 DNA ligase (NEB, M0202)) were added, mixed by inverting the samples and incubated at 18°C overnight with slow rotation in an oven. The next day, 25 µl were taken as ligation control and samples were spun down at 5000 g for 5 minutes. After the pellets were resuspended in 600 µl of Tris-HCl (10 mM, pH 7.5), de-crosslinking was performed by addition of 25 µl of proteinase K and 60 µl of 10% SDS, and incubation at 55°C for 30 minutes, succeeded by addition of NaCl and incubation at 68°C for 2 hours. DNA was precipitated by mixing the samples with 750 µl of pure ethanol and 75 µl of 3M sodium acetate (pH 5.2), followed by incubation at -80°C for 20 minutes. The precipitated DNA was pelleted by centrifugation at 16000 g for 15 minutes at 2°C. Samples were washed twice with 800 µl of 70% ethanol, then resuspended in 130 µl Tris-HCl (pH 8) and incubated at 37°C for 15 minutes to fully dissolve the DNA.
Succeeding to shearing the DNA to a size of 300-500 bp with a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 6 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C), the samples were transferred to low-bind tubes and diluted in 100 µl of water. Per sample, 150 µl of Dynabeads MyOne Streptavidin T1 beads(Life technologies, 65602) were  washed in  Tween Washing Buffer (TWB: 5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, 0.5% Tween-20), resuspended in 300 µl 2X Binding Buffer (BB: 10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 2M NaC), mixed with the sheared DNA and incubated at RT for 15 min with rotation to bind biotinylated DNA. The beads were washed twice with 600 µl TWB, (for all washing steps with TWB, the tubes are heated to 55° for 2 minutes) and afterwards washed once with T4 DNA ligase buffer (NEB, B0202). In order to repair the sheared ends of DNA and to remove biotin from unligated ends, the beads were resuspended in 100 µl of mastermix (0.88x NEB T4 DNA ligase buffer with 10 mM ATP, 0.5 mM dNTP mix, 0.5 U/µl PNK (NEB, M0201), 0.07 U/µl T4 DNA polymerase (NEB, M0203), 0.05 U/µl DNA polymerase I, Large (Klenow) Fragment (NEB M0210)) and incubated for 30 minutes at RT.  Beads were washed twice with 600 µl of TWB and transferred to a new low-bind tube. Subsequent to washing the beads once with 200 µl NEBuffer 2, they were resuspended in 100 µl dATP attachment master mix (0.9X NEBuffer 2, 0.5 mM ATP, 0.25 NEB Klenow exo minus (NEB, M0212) and incubated for 30 minutes at 37°C. Again, the beads were washed twice with TWB,  once with 100 µl of NEB Quick ligation buffer (NEB B6058) and transferred to a new tube. After resuspension of the beads in 50 µl of NEB Quick ligation buffer, 2 µl of NEB DNA Quick ligase (NEB M2200) and 3 µl of universal adapter from NEBNext® Ultra™ DNA Library Prep Kit for Illumina and incubated at RT for 15 minutes. The suspension was mixed with 3 µl of User enzyme and incubated at 37°C for 15 minutes. Thereafter, beads were washed twice with TWB, washed once with 100 µl 10 mM Tris-HCl (pH 7.5) and transferred to a new low-bind tube, and finally resuspended in 50 µl 10 mM Tris-HCl (pH 7.5). Next, the HiC library was directly amplified from the T1 beads according to Illumina protocols (Illumina, 2007). After amplification was complete, the volume of the library was adjusted to 250 µl with 10 mM Tris-HCl (pH 7.5). Following to addition of 137.5 µl of AMPure XP beads, the reaction mix was incubated 5 minutes at RT. Beads were reclaimed via a magnet and the supernatant was again subjected to 37.5 µl of AMPure XP beads with 5 minutes incubation at RT. Beads were captured via a magnet and washed twice with 700 µl of 70% ethanol. After air-drying the beads, the bound DNA was eluted by addition of 25 µl of Tris (10 mM, pH 7.5) and incubation for 5 minutes at RT. Once again, the beads were separated with a magnet and the supernatant transferred to a new tube. The libraries were sequenced on an Illumina HiSeq4000 with ca. 200 million reads (75 bp, paired-end) per sample.


title: 1001702104_O21


title: MEF_12


title: 1001701101_A14

value: NK cell


title: 1001702104_O2

value: B cell


title: 1001701101_A13


title: HiC_WT_E115-LB-Rep1


title: MEF_10


title: 1001701101_A11


title: HiC_WT_E115-LB-Rep2


title: 1001702104_O19


title: 1001702104_O18


title: MEF_9


title: 1001701101_A12


title: 1001701101_A10


title: WT_7D_704503

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Bioinformatic analysis was performed using CGAT Pipelines and tools (https://github.com/CGATOxford/CGATPipelines). Reads were aligned to the mm10 mouse genome using hisat2 version 2.1.0, and reads were quantified over feature annotations (ensemble81) using featureCounts program version 1.4.6 within the Subread software package.  DESeq2 was used for statistical analysis of the differential expression for each gene between wild-type and ZIP7P198A/P198A mutants.
Genome_build: mm10

molecule: polyA RNA

source_name: B cells

growth_protocol: BM cells of WT and P198A/P198A mutant mice (generated by CRISPR/Cas9) were injected into lethally irradiated CD45.1 mice to generate straight chimeras. After 8 weeks reconstitution, 5 WT mice and 5 P198A/P198A mutant straight chimeras mice BM were freshly isolated for the experiment.

extract_protocol:
100 cells per sample were directly sorted into ice cold cell lysis buffer (0.4% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor, 4 x107 dilution of ERCC spike in control, comprising a pre-formulated blends of 92 transcripts, derived and traceable from NIST-certified DNA plasmids), 2.5mM dNTPs (Thermo-Fisher), 2.5µM Oligo (Oligo-dT30VN.) and immediately frozen in dry ice.Sorted cells were processed using the Smart-seq2 protocol with minor changes
Indexing of the samples was performed using the Nextera XT DNA Sample Preparation Index kit (24 index primers, manufacturer (Illumina)), according to manufacturer’s instructions.

treatment_protocol: BM cells from straight chimeras were stained with B220,CD43,CD45.1,CD45.2,CD24,BP-1,IgM and IgD Abs.Cells were sorted using a FacsARIA III (BD), using the following gating strategy: viable, B220+CD43+CD45.1-CD45.2+CD24+BP1- (FrB/pro-B); B220+CD43-CD45.1-CD45.2+IgM-IgD- (FrD/late preB) and viable, B220+CD43-CD45.1-CD45.2+IgM+IgD- (FrE/Immature)

value: bone marrow  cell

value: B cells

tag: tag

value: Wild type


title: WT_7E_704504


title: 1001702104_O17

value: blood


title: MEF_8


title: 1001701101_A9


title: WT_7B_704517


title: 1001702104_O20

value: unknown


title: MEF_7


title: 1001702104_O15

value: F


title: 1001702104_O16

value: severe dengue


title: WT_7C_704502


title: 1001701101_A8


title: 1001702104_O14


title: MEF_5

value: embryonic fibroblasts


title: MEF_11

value: growth medium


title: MEF_6


title: WT_6E_703508


title: 1001702104_O13


title: WT_6D_703507


title: 1001701101_A5

value: M


title: MEF_4


title: WT_6C_703506


title: 1001702104_O12


title: MEF_3


title: WT_6B_703505


title: 1001701101_A4

value: control


title: 1001701101_A3


title: MEF_2


title: 1001702104_O10


title: 1001701101_A7


title: MEF_1


title: WT_3E_702504


title: 1001701101_A2

value: monocyte


title: mchon_66

source_name: mouse chondrocytes

value: limb cartilage

value: chondrocytes


title: WT_3D_702503


title: 1001702104_O1


title: 1001701101_A6

value: NKT cell


title: VLN_16R

city: pittsburgh

first: Leonardo

last: D'aiuto

state: pa

address: 3811 O'Hare st

department: psychiatry

country: USA

institute: UPMC

data_processing:
sequenced reads were processed and aligned using CLCbio v9.5.3
Sequences were trimmed based on quality score using the modified-Mott trimming algorithm as implemented in CLC bio software, using a trim cutoff error probability of 0.05.  Ambiguous bases were trimmed using a post trim maximal ambiguous base cutoff of 2.  The trimmed reads were then mapped to the human genome GRCh38/hg38, using sequence and annotation provided by Ensembl (release 82). Approximately 93% of reads were mapped in pairs (SD=0.45) across all samples, and 98.4% of reads were mapped in total (SD=0.46).  The remaining unmapped reads were collected and mapped to the Human Herpesvirus strain KOS genome (GenBank: JQ780693.1).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: csv format file with total counts, RPKM, TPM and CPM for each sample

source_name: iPSC line

growth_protocol: hiPSC-neurons were cultured in mTeSR1 medium. hiPSC-neurons were generated as previously described (D’Aiuto et al. Organogenesis. 2014;10(4):365-77).

extract_protocol:
At 12 hpi, the cellular RNA was extracted (RNeasy Mini Kits, Qiagen) and quantified using Agilent 4200 TapeStation (Agilent Technologies).
Total RNA libraries were generated using the Illumina TruSeq Stranded Total RNA Sample Preparation Guide, Revision E. The first step involved the removal of ribosomal and mitochondrial RNA using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, remaining RNA was fragmented using divalent cations under elevated temperature, which were then copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H.  Subsequently, a single adenosine base was added to each of the cDNA fragments  followed by ligation of an adapter.  The products were purified and enriched with PCR to create the final cDNA library.  The cDNA libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorimeter. Quality was examined using an Agilent Bioanalyzer Tapestation 2200. The cDNA libraries were pooled at a final concentration 1.8pM.

treatment_protocol: We used a genetically engineered HSV-1 KOS strain that expresses enhanced green fluorescent protein (EGFP) and red fluorescent protein (RFP) under the control of immediate early and late gene promoters, respectively (33).  To determine the optimal conditions for evaluating drug effects, hiPSC-neurons cells were infected for 2 hours (multiplicity of infection, MOI=0.3), after which the inocula were replaced with media containing R430 (10 µM) or vehicle (DMSO).  Separately, cells were incubated in media containing R430 (10 µM) or vehicle in the absence of HSV-1. All assays were conducted in triplicate.  Cells were harvested after 6 hours post infection (hpi), 12 hpi, or 24 hpi, DNA was extracted using (QIAamp DNA Mini Kit, (Qiagen) and DNA conentrations were estimated. Subsequently, the EGFP locus was amplified to estimate viral copy number using custom primers (34).  A significant increase in viral copy number was noted in vehicle treated cells after 12h and 24h, but not after 6h. Substantial reduction in viral copy number was found following incubation with R430 at 12h or 24h.  The 12h incubation period was therefore selected for subsequent studies examining gene expression

value: iPSC derived neurons

tag: infection status

value: HSV-1 infected

tag: drug status

value: with R430


title: 1001702104_N9


title: WT_3C_702502

value: bone marrow  cell

value: B cells


title: 1001702104_N8

value: blood


title: WT_2E_701508

value: Wild type


title: mchon_65


title: WT_3B_702517


title: 1001702104_N7

value: F


title: 1001701101_A1

value: T cell


title: VLN_14R


title: WT_2D_701507


title: mchon_63


title: 1001702104_N6

value: unknown

value: severe dengue


title: 1001702104_O11


title: VLN_12R

value: no drug


title: mchon_62

value: growth medium


title: 1001702104_N5


title: 1001702104_N4


title: mchon_61


title: WT_2B_701505


title: mchon_59


title: WT_1E_701504


title: VLN_08R

value: uninfected


title: VLN_10R


title: WT_1D_701503


title: VLN_13R


title: mchon_64

value: limb cartilage


title: WT_2C_701506


title: mchon_58

value: chondrocytes


title: VLN_11R


title: WT_1C_701502


title: 1001702104_N3


title: 1001702104_N23


title: 1001702104_N22


title: VLN_06R


title: VLN_05R


title: 1001702104_N21

value: monocyte


title: mchon_57


title: mchon_56


title: WT_1B_701517


title: KO_9E_705504

value: P198A/P198A mutant


title: 1001702104_N20


title: VLN_03R

value: iPSC derived neurons


title: KO_9D_705503


title: mchon_60


title: 1001702104_N2


title: VLN_01R


title: mchon_54


title: KO_9C_705502


title: mchon_53


title: 1001702104_N18


title: KO_8E_704508


title: mchon_52


title: 1001702104_N17

value: B cell


title: 1001702104_N16


title: mchon_51


title: VLN_04R


title: mchon_50


title: KO_8D_704507

value: bone marrow  cell


title: mchon_49


title: KO_8B_704505

value: B cells


title: 1001702104_N15

value: blood


title: mchon_55


title: 1001702104_N14


title: KO_5E_703504


title: 1001702104_N13


title: 1001702104_N19


title: mchon_47


title: KO_9B_705517


title: KO_5D_703503


title: 1001702104_N12


title: mchon_46


title: KO_5C_703502


title: KO_8C_704506


title: 1001702104_N11


title: KO_5B_703517


title: mchon_45


title: KO_4E_702508


title: mchon_43


title: 1001702104_N10

value: pDC


title: 1001702104_N1

value: F


title: mchon_44


title: GM74 Left ovary

type: genomic

city: Herston

first: Jamie

middle: R

last: Kutasovic

state: QLD

address: UQCCR, Building 71/918

department: Faculty of Medicine

institute: The University of Queensland

description: Whole genome copy number profile of ovarian metastasis

hyb_protocol: Labelled DNA was co-hybridised with Cy3 labelled normal female genomic DNA to the Agilent-022060 SurePrint G3 Human CGH Microarray (Platform GLP10150; 4x180k). The samples were hybridised on the array for 40 hours before microarray washing and scanning.

scan_protocol: Slides were scanned on an Agilent C DNA scanner, with profile G3_CGH with a 3 μm resolution.

data_processing: Data was extracted from scanned images and processed using Feature Extraction software (v10.7; Agilent Technologies) and the default protocol CGH_107_Sep09

source_name: Left ovary

label_protocol: 500 ng of sample DNA was labelled with Cy5 (and the female reference DNA labelled with Cy3) following the ULS protocol (Manual part number G4410-90020, Version 3.4, July 2012. Agilent Technologies, Inc).

extract_protocol: DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Cat # 69506), following overnight sodium thiocyanate (1M) incubation and 3 days proteinase K (Invitrogen, Cat #25530049) digestion at 55°C. Qiagen AW2 buffer was replaced with two 70% ethanol washes.

treatment_protocol: Surgical specimen processed in formalin and embedded in paraffin wax

tag: gender

value: Female

tag: dna source

value: FFPE tumor

tag: disease state

value: Breast cancer

tag: tumor type

value: Ovarian metastasis

source_name: normal female genomic DNA

value: normal reference DNA


title: GM78 Breast

description: Whole genome copy number profile of primary breast tumor

source_name: Breast

tag: patient id

value: Primary breast tumor

tag: tissue


title: mchon_48

value: limb cartilage

tag: cell type

value: growth medium


title: GM63 Right ovary

source_name: Right ovary


title: mchon_42

value: chondrocytes


title: 1001702104_M8

tag: Sex

tag: diseaseseverity

value: severe dengue

tag: numberhumanuniquelymappedreads


title: KO_4C_702506

value: P198A/P198A mutant


title: GM78 Left ovary


title: GM82 Left ovary


title: GM63 Left ovary


title: 1001702104_M9

value: unknown

tag: numbervirusreads

tag: age


title: mchon_41

tag: strain

tag: passages

tag: treatment


title: GM74 Breast


title: KO_4B_702505

value: bone marrow  cell

tag: tag


title: mchon_40

tag: time


title: 1001702104_M6


title: KO_10D_705507

value: B cells


title: KO_10E_705508


title: 1001702104_M5

value: blood


title: KO_10C_705506


title: 1001702104_M4


title: GM59 Breast

tag: gender


title: GM59 Right ovary

tag: dna source


title: 1001702104_M3


title: mchon_37


title: mchon_39


title: 1001702104_M23

value: B cell


title: KO_10B_705505


title: mchon_35


title: GM50 Left ovary

tag: disease state


title: mchon_34


title: RNA-Seq-A

city: Columbus

first: Guramrit

last: Singh

state: OH

address: 484 W 12th Ave, BioSci, B211

department: Molecular Genetics

institute: Ohio State University

description: ribosomal RNA removed with Ribo-Zero kit (Illumina, Cat# MRZH116) prior to base hydrolysis of RNA

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing
Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters -m 20 --discard-untrimmed then mapped to hg38 whole genome using tophat v2.1.1 with parameters -p 12
Multi-mapped reads were removed based on tophat alignment score (< 50) and PCR duplicates were removed based on random barcodes
Aligned reads were checked for overlap against misc. RNA annotations (miRNA, Mt_rRNA, Mt_tRNA, rRNA, scaRNA, snoRNA, snRNA, and tRNA) using bedtools intersect v2.25.0 with parameters -s -c -F 0.51 -sorted and overlapping reads were removed
Coverage data was generated using bedtools intersect v 2.25.0 with parameters -s -c -F 0.51 -sorted
Genome_build: hg38
Supplementary_files_format_and_content: Mabin_etal_processedData.xlsx contains tab delimited overlap count results for the pulldown experiments

source_name: Human embryonic kidney cells

growth_protocol: Human HEK293 Flp-In Trex cell lines expressing FLAG-tagged exon junction complex components were cultured in Dulbecco's modified eagle medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and 1 % penicillin-streptomycin.

extract_protocol:
Cells were chemically crosslinked with 0.1% formaldehyde and total cell extracts were prepapred in denaturing lysis buffer.  In case of some samples, cells were left uncrossllinked and total extracts were prepared in a non-denaturing isotonic lysis buffer. All extracts were clarified at 15000 x g prior to isolation of EJC via FLAG-affinity purification.
Libraries were prepared using a custom protocol described in detail in Gangras et al., Methods Mol Biol. 2018;1680:1-28. Briefly, a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription (RT) product, which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.

treatment_protocol: In case of some RIP-Seq samples, the cell lines were treated with translation inhibitor cycloheximide at 100 μg/ml for 3 hours before cell harvesting.

tag: cell line

value: HEK293 Flp-In Trex (ThermoFisher, # R78007)

tag: fusion protein stably expressed

tag: cycloheximide treatment

tag: formaldehyde crosslinking

tag: ripit (1st antibody)

tag: ripit (2nd antibody)


title: RNA-Seq-B


title: GM57 Breast

tag: patient id

value: Female

tag: tumor type

tag: tissue


title: GM45 Right ovary

value: FFPE tumor


title: mchon_36

tag: strain

tag: cell type


title: GM63 Breast

value: Breast cancer


title: mchon_38

tag: passages

tag: treatment


title: RNPS1-EIF4A3-XL-B (+CHX)

description:
Other (protein-bound RNA)
Input RNA was RNase I footprints of complexes containing FLAG-RNPS1 and EIF4A3 proteins

value: 3 hours pre-harvest, 100μg/ml

value: 0.1 % formaldehyde for 10 min before cell lysis

value: anti-FLAG M2 (Sigma, Cat# A2220)

value: Human EIF4A3 (Bethyl, Cat# A302-980A)


title: 1001702104_M21

tag: Sex

value: F

tag: diseaseseverity

tag: numberhumanuniquelymappedreads

tag: numbervirusreads

tag: age


title: RNPS1-EIF4A3-XL-A (+CHX)

tag: cell line

tag: fusion protein stably expressed


title: GM49 Right ovary

tag: gender

tag: dna source

tag: disease state

value: Ovarian metastasis

value: normal reference DNA


title: 1001702104_M20

tag: patient id

value: severe dengue


title: GM45 Left ovary

tag: tumor type


title: GM39 Right ovary

tag: tissue


title: 1001702104_M22

value: unknown


title: GM39 Left ovary


title: CASC3-EIF4A3-XL-B (+CHX)

description:
Other (protein-bound RNA)
Input RNA was RNase I footprints of complexes containing FLAG-CASC3 and EIF4A3 proteins

tag: cycloheximide treatment

tag: formaldehyde crosslinking

tag: ripit (1st antibody)

tag: ripit (2nd antibody)


title: GM36 Breast

value: Primary breast tumor


title: 1001702104_M2

tag: cell type

tag: Sex


title: mchon_32

tag: strain

value: limb cartilage

value: chondrocytes

tag: passages

tag: treatment

value: growth medium

tag: time


title: mchon_33


title: mchon_31


title: 1001702104_M19

value: blood

value: monocyte

tag: diseaseseverity

tag: numberhumanuniquelymappedreads

tag: numbervirusreads

tag: age


title: CASC3-EIF4A3-XL-A (+CHX)

tag: cell line

value: HEK293 Flp-In Trex (ThermoFisher, # R78007)

tag: fusion protein stably expressed


title: GM29 Breast

tag: patient id

tag: gender

value: Female

tag: dna source

value: FFPE tumor

tag: disease state

value: Breast cancer

tag: tumor type

tag: tissue


title: mchon_30

tag: cell type


title: RNPS1-EIF4A3-XL-B

tag: cycloheximide treatment

tag: formaldehyde crosslinking

value: 0.1 % formaldehyde for 10 min before cell lysis

tag: ripit (1st antibody)

value: anti-FLAG M2 (Sigma, Cat# A2220)

tag: ripit (2nd antibody)


title: RNPS1-EIF4A3-XL-A

value: Human EIF4A3 (Bethyl, Cat# A302-980A)


title: mchon_29

tag: strain

tag: passages

tag: treatment

tag: time


title: 1001702104_M18

tag: Sex

value: F

tag: diseaseseverity

tag: numberhumanuniquelymappedreads

tag: numbervirusreads

tag: age


title: 1001702104_M17

tag: patient id


title: 1001702104_M16


title: CASC3-EIF4A3-XL-B

tag: cell line

tag: fusion protein stably expressed


title: GM16 Right ovary

tag: gender

tag: dna source

tag: disease state

tag: tumor type

value: Ovarian metastasis

tag: tissue

value: normal reference DNA


title: mchon_27

tag: strain

tag: cell type


title: CASC3-EIF4A3-XL-A

tag: cycloheximide treatment

tag: formaldehyde crosslinking

tag: ripit (1st antibody)

tag: ripit (2nd antibody)


title: 1001702104_M15

value: unknown

tag: Sex

tag: diseaseseverity

value: severe dengue

tag: numberhumanuniquelymappedreads


title: mchon_26

value: limb cartilage

tag: passages

tag: treatment

tag: time


title: MAGOH-RNPS1

description:
Other (protein-bound RNA)
Input RNA was RNase I footprints of complexes containing FLAG-MAGOH and RNPS1 proteins

tag: cell line

tag: fusion protein stably expressed

value: FLAG-MAGOH

value: Human RNPS1 (Sigma, Cat# HPA044014)


title: GM16 Left ovary

tag: patient id

tag: gender

tag: dna source

tag: disease state


title: 1001702104_M14

tag: tissue

value: blood

tag: cell type

tag: numbervirusreads

tag: age


title: mchon_25

tag: strain

value: chondrocytes

value: growth medium


title: mchon_28


title: RS

city: Shanghai

first: Zhiyong

last: Mao

address: 1239 Siping Road

institute: Tongji University

data_processing:
Raw reads were aligned to human (GRCh37) genome by STAR v2.5.3a with default parameter.
Raw reads which barcode base quality were less than 10 would be filtered.
Barcode and UMI extraction was performed using the Drop-seq tools softare version 1.2
A UMI counts expression matrix was generated by the Drop-seq tools software version 1.2
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include UMI counts of each sample

source_name: skin fibroblast cell

extract_protocol:
Cells and barcoded beads were encapsulated into droplets of about 1nl in size. Cells were lysed and RNA were captured by barcoded beads in droplets. Droplets were then breaked to collect beads. Beads with captured RNA were reverse transcribed and exonuclease-treated as described (Online-Dropseq-Protocol-v.-3.1, http://mccarrolllab.com/dropseq/).
cDNA libraries were amplified by aliquoting ~2000 beads into each PCR tubes, purified by using 0.6X AMpure Beads and quantified using Qubit. Equal amount of cDNA from each tube were pooled together, and sequencing libraries were prepared with Nextera XT tagmentation reactions using P5_TSO and Nextera_N7xx primer. Sequencing libraries were purified twice with 0.6x AMPure XP beads and once with 1x AMPure XP beads, quantified and sequenced (PE150) on Illumina HiSeq X10 sequencer using the custom primer Read1CustomSeqB.

value: HCA2 fibroblast cell

tag: phenotype

value: replicative senescent


title: MAGOH-CASC3

description:
Other (protein-bound RNA)
Input RNA was RNase I footprints of complexes containing FLAG-MAGOH and CASC3 proteins

value: HEK293 Flp-In Trex (ThermoFisher, # R78007)

tag: cycloheximide treatment

tag: formaldehyde crosslinking

tag: ripit (1st antibody)

tag: ripit (2nd antibody)

value: Human CASC3 (Bethyl, Cat# A302-472)


title: LowPD_50Gy

tag: passages

value: low population doubling

tag: treatment


title: GM06 Left ovary

value: Female

value: FFPE tumor

value: Breast cancer

tag: tumor type


title: GM06 Right ovary

tag: patient id

value: Ovarian metastasis

value: normal reference DNA


title: GM16 Breast

tag: gender

value: Primary breast tumor


title: RNPS1-EIF4A3

tag: cell line

tag: fusion protein stably expressed

value: anti-FLAG M2 (Sigma, Cat# A2220)

value: Human EIF4A3 (Bethyl, Cat# A302-980A)


title: mchon_24

tag: tissue

value: limb cartilage

tag: time


title: LowPD_Ctrl

tag: cell type


title: mchon_23


title: 1001702104_M12

value: blood

value: monocyte

tag: Sex

value: F

tag: diseaseseverity

value: severe dengue

tag: numberhumanuniquelymappedreads

tag: numbervirusreads

tag: age


title: HighPD_Ctrl

value: HCA2 fibroblast cell

tag: phenotype

value: high population doubling


title: 1001702104_M11

value: unknown


title: shRB1 RNASeq rep3

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6) on hg19.refseq.bed12
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: xls file for raw count and FPKM

source_name: Prostate cells

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

extract_protocol:
RNAs were extracted using RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

treatment_protocol: PC-3  cells were treated with 5 µM palbociclib for 24 hours.


title: mchon_22

tag: strain

value: chondrocytes

value: growth medium


title: MAGOH-EIF4A3

description:
Other (protein-bound RNA)
Input RNA was RNase I footprints of complexes containing FLAG-MAGOH and EIF4A3 proteins

value: HEK293 Flp-In Trex (ThermoFisher, # R78007)

value: FLAG-MAGOH

tag: cycloheximide treatment

tag: formaldehyde crosslinking

tag: ripit (1st antibody)

tag: ripit (2nd antibody)


title: shRB1 RNASeq rep1

tag: passages

tag: treatment


title: GM06 Breast

tag: patient id

tag: gender

value: Female

tag: dna source

value: FFPE tumor

tag: disease state

value: Breast cancer

tag: tumor type


title: CASC3-EIF4A3

tag: cell line

tag: fusion protein stably expressed

value: anti-FLAG M2 (Sigma, Cat# A2220)


title: mchon_21

tag: tissue

tag: cell type

tag: time


title: shRB1 RNASeq rep2


title: KO_4D_702507

value: bone marrow  cell

value: B cells

tag: tag

value: P198A/P198A mutant


title: 1001702104_M1

value: blood

tag: Sex

tag: diseaseseverity

tag: numberhumanuniquelymappedreads

tag: numbervirusreads

tag: age


title: 1001702104_M10

value: monocyte

value: F


title: 1001702104_M13

value: severe dengue


title: Sample_P16

city: Lexington

first: Shavahn

middle: C

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

data_processing:
The sequencing results were initially trimmed for adapters and quality using TrimGalore Version 0.4.4 (Babraham Bioinformatics; www.bioinformatics.babraham.ac.uk).
The sequences were mapped to EquCab2.0 using STAR-2.5.2b (github.com/alexdobin/STAR).
Final quantification at the gen level was performed by analyzing the BAM files in cufflinks using the Equus_caballus_ENSEMBL_88 gtf file as Guide.
Genome_build: EquCab2.0
Supplementary_files_format_and_content: normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Placenta

extract_protocol:
Isolation of RNA from tissue was performed using RNeasy Mini Kit (Qiagen, Gaithersburg, MD, USA), per manufacturer’s instructions.  After extraction, RNA was analyzed by NanoDrop® (Thermo Fisher Scientific) and Bioanalyzer® (Agilent, Santa Clara, CA, USA) to evaluate concentration, purity and integrity.  All samples had a 230/260 ratio > 1.8, a 260/280 ratio > 2.0 and an RNA integrity number > 8.0.
Library preparation was performed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), as per manufacturer’s instructions.  The adapter for Read 1 was AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG, with NNNNNN signifying the index sequence.  The read 2 adapter was AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT.  All reads were quantified with qPCR.  Sequencing was performed on a HiSeq 4000 (Illumina) using a HiSeq 4000 sequencing kit version 1, generating 150 bp paired-end reads.  FASTQ files were generated and demultiplexed using bcl2fastq v2.17.1.14 Conversion Software (Illumina).

treatment_protocol: Mares were bred via either pasture breeding or artificial insemination, with pregnancy confirmed by transrectal ultrasonography between 14 to 35 days of gestation. Gestational age was determined by date of ovulation if known, otherwise, the size and morphology of the embryo was used

value: chorioallantoic membrane


title: shControl RNASeq rep3

tag: passages

tag: treatment

value: shControl


title: mchon_20

tag: strain

value: limb cartilage

value: chondrocytes


title: shControl RNASeq rep2


title: 1001702104_L9

tag: patient id

value: unknown


title: Sample_O15


title: 1001702104_M7


title: GM50 Right ovary

tag: gender

tag: dna source

tag: disease state

value: Ovarian metastasis

value: normal reference DNA


title: 1001702104_L8


title: shControl RNASeq rep1


title: Sample_M13


title: mchon_19

value: growth medium


title: 1001702104_L7


title: PD0332991 RNASeq rep2


title: Sample_L12


title: mchon_18


title: mchon_16


title: Sample_K11


title: PD0332991 RNASeq rep3


title: mchon_17


title: DMSO RNASeq rep3

value: DMSO


title: 1001702104_L6


title: 1001702104_L5


title: Sample_I9


title: mchon_15


title: 1001702104_L3


title: mchon_14


title: PD0332991 RNASeq rep1


title: 1001702104_L4


title: mchon_13


title: Sample_H8


title: 1001702104_L23


title: DMSO RNASeq rep2


title: DMSO RNASeq rep1


title: Sample_N14


title: mchon_12


title: Sample_J10


title: 1001702104_L22


title: Sample_G7


title: 1001702104_L21


title: 1001702104_L20


title: mchon_10


title: 3D-CCM1-6hrs

city: Atlanta

first: Denis

last: Tsygankov

state: GA

address: North Ave NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

data_processing:
Quality control and adapter trimming: BBDuk, BBTools package Version 35.92. Values of parameters: ktrim=r k=27 hdist=1 edist=0 mink=4 qtrim=rl trimq=30 minlength=50 qin=33
Transcriptome alignment: TopHat2 v2.1.1 (human genome build GRCh38). Values of parameters: --no-coverage-search --b2-very-sensitive --no-novel-juncs
Reads counting and ranking of differentially expressed genes: GFOLD. Cutoff for generalized fold change: 0.3. Comand for reads counting: gfold count -ann [genome annotation] -tag [SAM file with mapped reads] -o [output file]. Command for identification of differentially expressed genes: gfold diff -s1 [reads counts for sample 1] -s2 [reads counts for sample 2] -suf .read_cnt -o [output_file.diff]
Genome_build: Human genome GRCh38
Supplementary_files_format_and_content: Tab-delimited text files generated by GFOLD, include GeneSymbols, GeneNames, GFOLD values, RPKM values and other information

growth_protocol: Human umbilical cord endothelial cells (HUVEC) were maintained in EGM-2 medium at 37°C/5% CO2 and passaged every 3 to 4 days for up to 6 passages at a 1:5 sub-culturing ratio.  For tube formation experiments, 4.5-5x103 cells were plated into each well of angiogenesis µ-slides coated with 10 µl of growth factor reduced phenol red-free Matrigel, and incubated for up to 18 hrs.

extract_protocol:
Total RNA was extracted using RNeasy extraction kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol. RNA was reverse-transcribed using the high-capacity cDNA kit (Life Technologies, Carlsbad, CA, USA). The analysis was done StepOnePlus™ Real-Time PCR System (Applied Biosystems, Foster City, CA), and the level of transcripts was quantified using TaqMan probes (Applied Biosystems): KRIT1 Hs01090981_m1; CCM2 Hs01123856_m1; PDCD10 Hs00200578_m1; TBP Hs00427620_m1. Fold change in gene expression was determined using ΔΔCt algorithm.
HUVEC cells were transfected with non-targeting siRNA or siRNA against krit1, ccm2, and pdcd10 genes as described above. 48 hrs after transfection cells were plated on growth factor reduced Matrigel, and incubated for 2 hrs (initial stages of endothelial tubule formation) or 6 hrs (advanced stages of tubule formation). Total RNA was isolated from each culture (control, and siRNA against krit1, ccm2, and pdcd10) cells cultured on the 2D (Matrigel-coated plastic), and in 3D (Matrigel) substrate, using RNAeasy kit (Qiagen, Valencia, CA, USA) per the manufacturer’s instructions. RNA quality control was performed by studying the relative intensity of 18s and 28s rRNA bands using an Agilent 2100 Bioanalyzer and RNA6000 Pico LabChip Kit (Agilent Technologies). Between 200ng and 1ug of RNA were used directly in the TruSeq mRNA stranded kit (Illumina, San Diego, CA) for isolation of mRNA from total RNA, generation of ds cDNA and preparation of libraries. The cDNA was quantified using the Qubit HS DNA kit (Thermo Fisher Scientific, Rockford, IL), and cDNA libraries were prepared using a TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA). The samples were run on a NextSeq 500 instrument (Illumina, San Diego, CA) with a read length of PE75bp.

treatment_protocol: Cells were transfected with 50 nM siRNA against human krit1 (LQ-003825-00), ccm2 (LG-014728-01), and pdcd10 (LQ-004436-00), or control non-targeting siRNA (D-001810-01-05), using DharmaFECT 4 transfection reagent. Gene expression was analyzed at 48 hrs, protein expression at 72 hrs after transfection, and phenotypic studies were conducted 60-72 hrs after transfection.

tag: cell line

value: HUVEC

tag: sirna for gene knockdown

tag: substrate for cultivation

value: Matrigel

tag: time of incubation

value: 6 hours


title: mchon_11

tag: tissue

tag: cell type

tag: time


title: Sample_F6


title: Sample_E5


title: 3D-CCM3-2hrs

value: 2 hours


title: 3D-NT-6hrs

value: non-targeting siRNA (D-001810-01-05)


title: Sample_D4


title: mchon_9


title: Sample_C3


title: 1001702104_L19

value: blood

tag: Sex

tag: diseaseseverity

tag: numberhumanuniquelymappedreads


title: Sample_B2


title: 1001702104_L2

value: F

tag: numbervirusreads

tag: age


title: 1001702104_L18

value: severe dengue


title: 3D-CCM2-2hrs


title: mchon_6

tag: strain

tag: passages

tag: treatment


title: 3D-CCM1-2hrs


title: Sample_A1

value: chorioallantoic membrane


title: mchon_5


title: 1001702104_L17

tag: patient id


title: SM3_S6

city: Leeds

first: Christopher

middle: Paul

last: Randall

state: West Yorkshire

address: Clarendon Way

department: Faculty of Biological Sciences

institute: University of Leeds

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptors and based on quality score, then mapped to the S. aureus 8325 sequence using CLC genomics workbench version 8
Genome_build: Staphylococcus aureus NCTC 8325
Supplementary_files_format_and_content: Tab delimited text files provide raw counts of sequencing reads to features of interest

organism: Staphylococcus aureus

extract_protocol:
RNAprotect (Qiagen) was added to cultures of each organism at 2x culture volume to stabilise RNA. Total RNA was extracted using the RNAeasy midi kit (Qiagen) according to manufacturer's instructions, with the exception that cells were first treated with lysostaphin (200 ug/ml) and proteinase K (40 ug/ml) for 90 and 10 minutes, respectively. Illumina TruSeq RNA Sample Prep Kit v2 was used for library creation with 1 ug of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: NsaS A208E

tag: growth stage

value: Exponentially-growing culture from tryptic soya broth


title: 3D-NT-2hrs

tag: cell line

tag: sirna for gene knockdown

tag: substrate for cultivation


title: 3D-CCM3-6hrs

tag: time of incubation


title: 1001702104_L16

tag: tissue

tag: cell type


title: mchon_4

value: limb cartilage

value: chondrocytes

tag: time


title: 2D-CCM3

value: Matrigel-coated plastic


title: mchon_8


title: SM2_S5


title: 1001702104_L15

value: unknown

tag: Sex

tag: diseaseseverity

tag: numberhumanuniquelymappedreads


title: 2D-CCM1


title: mchon_7

tag: strain

value: growth medium


title: mchon_2

tag: passages


title: 2D-NT


title: SM1_S4


title: 1001702104_L14

tag: numbervirusreads

tag: age


title: 2D-CCM2


title: 1001702104_L13

tag: patient id

value: B cell


title: WT1_S7

source_name: WT_exponentially-growing culture

tag: strain background

tag: genotype/variation

value: wild-type


title: mchon_3

tag: treatment


title: mchon_1


title: WT3_S9

tag: growth stage


title: Pik_shTsc22d1_1

status: Public on Nov 18 2018

city: Seattle

first: Slobodan

last: Beronja

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Standard Illumina outupt fastq
tophat map to mm9
Cufflinks determine FPKM
Genome_build: mm9
Supplementary_files_format_and_content: txt. Contain gene level FPKM output from Cufflinks

extract_protocol:
RNA extraction followed Qiaamp RNEAsy Kit protocol
RNA libraries were prepared for sequencing using NEBNext protocols

value: Mammary tumor from Pik3caH1047R/+ mammary gland transduced with lentivirus knockdown Tsc22d1.


title: Pik_shTsc22d1_3


title: Pik_shPten_2

value: Mammary tumor from Pik3caH1047R/+ mammary gland transduced with lentivirus knockdown Pten.


title: Pik_shPten_3


title: Pik_shTsc22d1_2


title: Pik_shPten_1


title: Pik_shCdkn2a_2

value: Mammary tumor from Pik3caH1047R/+ mammary gland transduced with lentivirus knockdown Cdkn2a.


title: Pik_2

value: Mammary tumor from Pik3caH1047R/+ mammary gland.


title: input_DNA_FF_rep4

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

country: Japan

institute: Yokohama City University

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were quality- and adaptor-trimmed using Trim Galore! version 0.4.0.
ChIP-seq reads were aligned to mouse genome using Bowtie version 1.1.1 with the parameters -n 2 -l 30 --best --strata -m 1.
RNA-seq reads were aligned to mouse genome using TopHat version 2.0.14 with default parameters except that a gtf reference file was used.
ChIP-seq and RNA-seq read count was done using SeqMonk version 0.30.2, correcting for total count per million reads.
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated using SeqMonk contain corrected RNA-seq read count for all genes and corrected ChIP-seq read count for TSSs ±0.5 kb.

source_name: GSCs

extract_protocol:
For ChIP-seq, cells were crosslinked and chromatin was prepared according to a previous report (Nat. Protoc. 3, 1032-1045) with modifications. For RNA-seq, total RNA was purified using Isogen (Nippon Gene), and treated with DNaseI to digest genomic DNA.
ChIP-seq libraries for H3K4me3, H3K27me3 and input (replicate 1 and 2) samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Libraries for H3K9me3 and input (replicate 3 and 4) were prepared using ThruPLEX DNA-seq Kit (Takara).  RNA-seq libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

value: germline stem cells (GSCs)

tag: genotype

tag: chip antibody

value: none (input)


title: H3K9me3_FF_ChIPSeq_rep1

tag: tissue

value: H3K9me3, Abcam, ab8898


title: input_DNA_FF_rep3


title: Pik_shCdkn2a_1


title: Pik_3


title: H3K9me3_FF_ChIPSeq_rep2


title: Pik_1


title: BT30

value: Mammary tumor from Pik3caH1047R/+ mammary gland transduced with pooled lentivirus encoding patient derived lesions.


title: Pik_shCdkn2a_3


title: BT29


title: BT23


title: BT28


title: BT25


title: BT26


title: BT19


title: BT21


title: BT20


title: BT18


title: BT14


title: BT24


title: BT27


title: BT12


title: BT13


title: BT16


title: BT11


title: BT10


title: BT09


title: BT22


title: BT04


title: BT05


title: BT06


title: BT03


title: BT07


title: BT08


title: BT02


title: BT01


title: Patient 5, cancerous colon tissue, biological replicate 2, technical replicate 1

city: Carlsbad

first: Milos

last: Babic

state: CA

address: 5922 Farnsworth Court, Suite 102

institute: BioSpyder Technologies Inc.

description:
Patient5_Cancer_bioRep2_techRep1
ColonCancerReplicatesMaster.csv

data_processing:
base calling on instrument with RTA
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
then bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing and generating fastqs
fastqs were aligned to a pseudo transcriptome using Bowtie, allowing up to 2 mis-matches.
Genome_build: TempO-Seq is a targeted sequencing assay, and sequencing results are aligned to a pseudo-transcriptome formed from known probe sequences (see Yeakley et al., PLoS One. 2017, 12(5):e0178302). For each species, the entire pseudo-transcriptome used for alignment is present in the corresponding master gene count files (Probe_ID and Probe_Sequence columns).
Supplementary_files_format_and_content: Probe_ID (genes) in column 1, Probe_Sequence used for alignment in column 2, Accession Number in column 3. Sample Names in row 1.

source_name: human colon FFPE

extract_protocol: TempO-Seq targeted expression assay. Addition of adapters by amplification.

value: colon

tag: sample preparation

value: human FFPE tissue

tag: input

value: 10 mm ^2, 5 micron thick


title: Patient 5, normal colon tissue, biological replicate 2, technical replicate 3

description:
Patient5_Normal_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 5, cancerous colon tissue, biological replicate 2, technical replicate 2

description:
Patient5_Cancer_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_M PND78-86 sample5

type: RNA

city: Ottawa

first: Nasrin

last: Khan

state: ON

address: 50 Colombine Driveway

country: Canada

institute: Health Canada

description: Biological replicate PND78-86, M control

hyb_protocol: Cy3 labeled reference cRNA (300 ng) was mixed with equal amounts of Cy5 labeled cRNA samples and hybridized to microarrays (Agilent Technologies Inc.) for 17 h in a hybridization chamber at 65°C with a rotation speed of 10 rpm.  Microarray slides were washed and scanned on an Agilent G2505C scanner at 3 μm resolution, according to manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

organism: Rattus norvegicus

source_name: Lver tissue

label_protocol: Total RNA (200 ng) from exposed and control groups, as well as universal reference total RNA (Agilent Technologies, Inc., Mississauga, ON, Canada) were used to synthesise complementary DNA (cDNA) and cyanine labeled complementary RNA (cRNA), using Low Input Quick Amp Labeling Kit (Agilent Technologies Inc., Mississauga, ON, Canada) according to manufacturer's instruction.  Cyanine-labeled cRNAs were synthesized using T7 RNA polymerase and in vitro transcription kits (Agilent Technologies Inc., Mississauga, ON, Canada).  cRNA was then purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada).  Cyanine 5-CTP (Cy-5) was used to label the sample, and universal reference RNAs were labeled with Cyanine 3-CTP (Cy-3).

extract_protocol: RNA was purified from liver samples using the QIAGEN RNeasy (QIAGEN, Valencia, CA) extraction kit according to the manufacturer’s protocol.  The RNase-free DNase (QIAGEN) kit was used for on column digestion of DNA during RNA purification process.  Purified RNA was eluted in 50µL RNase-free water and stored at -80°C until use.  The concentration of RNA was measured using a NanoDrop ND-1000 spectrophotometer (NanoDropTechnologies, Wilmington, DE).  The quality and integrity of RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Mississauga, ON, Canada) by determining RNA integrity number (RIN) and 28S/18S ratio.

treatment_protocol: This study investigated the effects of cross-fostering (adoption of a litter at birth) and maternal exposure to chemical mixtures that simulate human blood contaminant profiles on the hepatic transcriptome in male Sprague Dawley rats at 21 and 78-86 days of age. The cross-fostering procedure was included to study the effects of in utero exposure, postnatal exposure through nursing, and the complete developmental exposure from gestation day (GD) 0 until postnatal day (PND) 20.  The detailed protocol, systemic effects, the glucocorticoid stress response (Desaulniers et al., 2013 Toxicology, 308:20-33), DNA methylation and the contaminant residue profiles have been published previously (Desaulniers et al., 2017.  J. Toxicol Environ Health A, 80:32-52). Briefly, five groups were not cross-fostered and remain undisturbed with their mothers.  These include a control group (C) that received corn oil only; two groups were treated with the same chemical mixtures dissolved in corn oil [M: including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and methyl mercury (MeHg)] at two doses of 0.5 mg/kg/day (0.5M), and 1.0 mg/kg/day (M).  A group of dams were treated with a mixture of aryl hydrocarbon-receptor (AhR) agonists [including non-ortho-PCBs, polychlorinated-dibenzodioxins, and polychlorinated-dibenzofurans, at a total dose of 1.8 ng/kg/day based on tetrachloro-dibenzodioxin (TCDD)-toxic equivalent (TEQ)], and a final group was treated with 0.5M plus the AhR chemicals in the same mixture (0.5MAhR at 6.3 ng/kg/day TCDD-TEQ). 0.5MAhR group was used to test the effects of increasing abundance of AhR-agonists on the toxicity of the 0.5M mixture.  A large number of dams were included in the group M and C from which those that gave birth simultaneously were selected to create the four cross-fostered treatment groups with the following in utero/postnatal exposure: C/C, M/C, C/M, and M/M.  The first letter indicating the treatment of the biological mother, and the second letter refers to the treatment of the adopting mother.  For the current microarray study, only the group CC and MM were investigated.  To avoid potential confounding litter effects, the liver from one male per litter was collected per treatment group at PND21, and during the interval PND78-86.  In total, eight male pups from different litters for each treatment group were collected, wrapped in aluminium foil, and immediately flash frozen in liquid nitrogen.  The samples were then stored at -80°C until RNA isolation.

tag: gender

value: Male

value: Sprague-Dawley

value: M treated

value: Postnatal day78-86

source_name: Agilent Universal Rat reference RNA

tag: sample type

value: Reference

tag: cell type

value: 14 rat cell lines


title: Liver_Cross-fostered M PND78-86 sample2

description: Biological replicate PND78-86, MM treated

tag: strain

value: MM treated


title: Liver_Control PND78-86 sample11

description: Biological replicate PND78-86, control

value: Control


title: Liver_Cross-fostered control PND78-86 sample4

description: Biological replicate PND78-86, CC treated

value: CC treated


title: Liver_Cross-fostered control PND78-86 sample3


title: Liver_Cross-fostered control PND78-86 sample1


title: Liver_M PND78-86 sample4

description: Biological replicate PND78-86, M treated

hyb_protocol: Cy-3 labeled reference cRNA (300 ng) was mixed with equal amounts of Cy-5 labeled cRNA samples and hybridized to microarrays (Agilent Technologies Inc.) for 17 h in a hybridization chamber at 65°C with a rotation speed of 10 rpm.  Microarray slides were washed and scanned on an Agilent G2505C scanner at 3 μm resolution, according to manufacturer's instructions.


title: Patient 5, normal colon tissue, biological replicate 2, technical replicate 1

description:
Patient5_Normal_bioRep2_techRep1
ColonCancerReplicatesMaster.csv


title: Liver_Control PND78-86 sample10

description: Biological replicate PND78-86, control


title: Liver_Control PND78-86 sample12

description: Biological replicate PND78-86, control


title: Liver_control PND78-86 sample8

description: Biological replicate PND78-86, control


title: Liver_Cross-fostered control PND78-86 sample2


title: Liver_M PND78-86 sample2


title: Liver_M PND78-86 sample6


title: Liver_M PND78-86 sample3


title: Liver_control PND78-86 sample5

description: Biological replicate PND78-86, control


title: Liver_Control PND78-86 sample9

description: Biological replicate PND78-86, control


title: Liver_control PND78-86 sample6

description: Biological replicate PND78-86, control


title: Patient 5, cancerous colon tissue, biological replicate 2, technical replicate 3

description:
Patient5_Cancer_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 5, normal colon tissue, biological replicate 2, technical replicate 2

description:
Patient5_Normal_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_control PND78-86 sample7

description: Biological replicate PND78-86, control


title: Patient 5, cancerous colon tissue, biological replicate 1, technical replicate 2

description:
Patient5_Cancer_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_M PND78-86 sample1


title: Liver_Cross-fostered M PND78-86 sample3


title: Patient 5, normal colon tissue, biological replicate 1, technical replicate 3

description:
Patient5_Normal_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 5, cancerous colon tissue, biological replicate 1, technical replicate 3

description:
Patient5_Cancer_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 5, normal colon tissue, biological replicate 1, technical replicate 2

description:
Patient5_Normal_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_Cross-fostered M PND78-86 sample1


title: Patient 5, normal colon tissue, biological replicate 1, technical replicate 1

description:
Patient5_Normal_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Liver_Control PND21 sample8

description: Biological replicate PND21, control

value: Postnatal day21


title: Patient 4, cancerous colon tissue, biological replicate 2, technical replicate 2

description:
Patient4_Cancer_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 4, cancerous colon tissue, biological replicate 2, technical replicate 3

description:
Patient4_Cancer_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 4, cancerous colon tissue, biological replicate 2, technical replicate 1

description:
Patient4_Cancer_bioRep2_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 4, normal colon tissue, biological replicate 2, technical replicate 3

description:
Patient4_Normal_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 4, normal colon tissue, biological replicate 2, technical replicate 2

description:
Patient4_Normal_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 5, cancerous colon tissue, biological replicate 1, technical replicate 1

description:
Patient5_Cancer_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 4, normal colon tissue, biological replicate 2, technical replicate 1

description:
Patient4_Normal_bioRep2_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 4, cancerous colon tissue, biological replicate 1, technical replicate 3

description:
Patient4_Cancer_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 4, cancerous colon tissue, biological replicate 1, technical replicate 1

description:
Patient4_Cancer_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 4, normal colon tissue, biological replicate 1, technical replicate 3

description:
Patient4_Normal_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Liver_Control PND21 sample5

description: Biological replicate PND21, control


title: Patient 4, normal colon tissue, biological replicate 1, technical replicate 1

description:
Patient4_Normal_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 4, cancerous colon tissue, biological replicate 1, technical replicate 2

description:
Patient4_Cancer_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 3, cancerous colon tissue, biological replicate 2, technical replicate 3

description:
Patient3_Cancer_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: BT31


title: Liver_0.5MAhR PND21 sample2

description: Biological replicate PND21, 0.5MAhR treated

value: 0.5MAhR treated


title: Liver_0.5MAhR PND21 sample4


title: Liver_Control PND21 sample6

description: Biological replicate PND21, control


title: Liver_M PND21 sample4

description: Biological replicate PND21, M treated

value: Postnatal day 21


title: Liver_AhR PND21 sample3

description: Biological replicate PND21, AhR treated

value: AhR treated


title: Liver_0.5M PND21 sample3

description: Biological replicate PND21, 0.5M treated

value: 0.5M treated


title: Liver_0.5MAhR PND21 sample1


title: Patient 3, cancerous colon tissue, biological replicate 2, technical replicate 2

description:
Patient3_Cancer_bioRep2_techRep2
ColonCancerReplicatesMaster.csv

value: colon


title: Liver_0.5MAhR PND21 sample3


title: Liver_M PND21 sample3

description: Biological replicate PND21, M treated


title: Liver_0.5M PND21 sample4


title: Liver_Control PND21 sample3

description: Biological replicate PND21, control


title: Liver_Control PND21 sample2

description: Biological replicate PND21, control


title: Patient 3, cancerous colon tissue, biological replicate 2, technical replicate 1

description:
Patient3_Cancer_bioRep2_techRep1
ColonCancerReplicatesMaster.csv

value: human FFPE tissue


title: Liver_AhR PND21 sample4

description: Biological replicate PND21, AhR treated


title: Liver_Control PND21 sample7

description: Biological replicate PND21, control


title: Liver_Control PND21 sample4

description: Biological replicate PND21, control


title: Liver_M PND21 sample1

description: Biological replicate PND21, M treated


title: Liver_M PND21 sample2

description: Biological replicate PND21, M treated


title: Liver_0.5M PND21 sample2


title: Liver_AhR PND21 sample2

description: Biological replicate PND21, AhR treated


title: Patient 3, normal colon tissue, biological replicate 2, technical replicate 3

description:
Patient3_Normal_bioRep2_techRep3
ColonCancerReplicatesMaster.csv

value: 10 mm ^2, 5 micron thick


title: Patient 4, normal colon tissue, biological replicate 1, technical replicate 2

description:
Patient4_Normal_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 3, normal colon tissue, biological replicate 2, technical replicate 2

description:
Patient3_Normal_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 3, normal colon tissue, biological replicate 2, technical replicate 1

description:
Patient3_Normal_bioRep2_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 3, cancerous colon tissue, biological replicate 1, technical replicate 3

description:
Patient3_Cancer_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Liver_0.5M PND21 sample1

value: Male


title: Patient 3, cancerous colon tissue, biological replicate 1, technical replicate 2

description:
Patient3_Cancer_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 3, cancerous colon tissue, biological replicate 1, technical replicate 1

description:
Patient3_Cancer_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Liver_Control PND21 sample1

description: Biological replicate PND21, control

value: Sprague-Dawley


title: Patient 3, normal colon tissue, biological replicate 1, technical replicate 2

description:
Patient3_Normal_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_M PND21 sample8

description: Biological replicate PND21, M treated

value: M treated


title: Liver_Cross-fostered M PND21 sample4

description: Biological replicate PND21, MM treated


title: Patient 2, cancerous colon tissue, biological replicate 2, technical replicate 3

description:
Patient2_Cancer_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: Liver_Cross-fostered M PND21 sample3

description: Biological replicate PND21, MM treated


title: Patient 3, normal colon tissue, biological replicate 1, technical replicate 1

description:
Patient3_Normal_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 2, cancerous colon tissue, biological replicate 2, technical replicate 2

description:
Patient2_Cancer_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_Cross-fostered M PND21 sample2

description: Biological replicate PND21, MM treated


title: Patient 2, normal colon tissue, biological replicate 2, technical replicate 2

description:
Patient2_Normal_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 2, normal colon tissue, biological replicate 2, technical replicate 3

description:
Patient2_Normal_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 2, cancerous colon tissue, biological replicate 2, technical replicate 1

description:
Patient2_Cancer_bioRep2_techRep1
ColonCancerReplicatesMaster.csv


title: Liver_M PND21 sample7

description: Biological replicate PND21, M treated


title: Liver_M PND21 sample6

description: Biological replicate PND21, M treated


title: Patient 2, cancerous colon tissue, biological replicate 1, technical replicate 3

description:
Patient2_Cancer_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 3, normal colon tissue, biological replicate 1, technical replicate 3

description:
Patient3_Normal_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Liver_M PND21 sample5

description: Biological replicate PND21, M treated


title: Patient 2, cancerous colon tissue, biological replicate 1, technical replicate 2

description:
Patient2_Cancer_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_AhR PND21 sample1

description: Biological replicate PND21, AhR treated


title: Patient 2, cancerous colon tissue, biological replicate 1, technical replicate 1

description:
Patient2_Cancer_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Liver_Control PND21 sample11

description: Biological replicate PND21, control


title: Liver_Cross-fostered control PND21 sample4

description: Biological replicate PND21, CC treated


title: Liver_Cross-fostered control PND21 sample3

description: Biological replicate PND21, CC treated


title: Liver_Cross-fostered M PND21 sample1

description: Biological replicate PND21, MM treated


title: Liver_Cross-fostered control PND21 sample2

description: Biological replicate PND21, CC treated


title: Liver_Control PND21 sample9

description: Biological replicate PND21, control


title: BT17

value: Mammary tumor from Pik3caH1047R/+ mammary gland transduced with pooled lentivirus encoding patient derived lesions.


title: Liver_Control PND78-86 sample4

description: Biological replicate PND78-86, control

value: Postnatal day78-86

value: Reference


title: Patient 1, cancerous colon tissue, biological replicate 2, technical replicate 3

description:
Patient1_Cancer_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: BT15


title: Liver_AhR PND78-86 sample3

description: Biological replicate PND78-86, AhR treated

value: 14 rat cell lines


title: Liver_Control PND21 sample10

description: Biological replicate PND21, control

value: Control


title: Patient 2, normal colon tissue, biological replicate 2, technical replicate 1

description:
Patient2_Normal_bioRep2_techRep1
ColonCancerReplicatesMaster.csv


title: Liver_Control PND21 sample12

description: Biological replicate PND21, control


title: Patient 1, cancerous colon tissue, biological replicate 2, technical replicate 1

description:
Patient1_Cancer_bioRep2_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 1, normal colon tissue, biological replicate 2, technical replicate 3

description:
Patient1_Normal_bioRep2_techRep3
ColonCancerReplicatesMaster.csv


title: Liver_AhR PND78-86 sample4


title: Patient 1, normal colon tissue, biological replicate 2, technical replicate 2

description:
Patient1_Normal_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_Control PND78-86 sample2

description: Biological replicate PND78-86, control


title: Liver_AhR PND78-86 sample1


title: Patient 1, normal colon tissue, biological replicate 2, technical replicate 1

description:
Patient1_Normal_bioRep2_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 2, normal colon tissue, biological replicate 1, technical replicate 3

description:
Patient2_Normal_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Liver_AhR PND78-86 sample2


title: Patient 2, normal colon tissue, biological replicate 1, technical replicate 2

description:
Patient2_Normal_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 1, cancerous colon tissue, biological replicate 1, technical replicate 3

description:
Patient1_Cancer_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: Patient 2, normal colon tissue, biological replicate 1, technical replicate 1

description:
Patient2_Normal_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Liver_Control PND78-86 sample3

description: Biological replicate PND78-86, control


title: Patient 1, cancerous colon tissue, biological replicate 1, technical replicate 2

description:
Patient1_Cancer_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 1, cancerous colon tissue, biological replicate 1, technical replicate 1

description:
Patient1_Cancer_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Patient 1, normal colon tissue, biological replicate 1, technical replicate 3

description:
Patient1_Normal_bioRep1_techRep3
ColonCancerReplicatesMaster.csv


title: 26Nef transfection tp2 [miRNA]

city: Washington

first: Michael

last: Bukrinsky

state: District of Columbia

institute: GWU

description:
sample that contains small RNAs produced into the culture supernatants in Nef transfection group during the time period between 48 and 72 hrs post-transfection (sample collection were done in January 2018).
26N2
small RNAs

data_processing:
A minimum of 17 million 50bp sequencing reads were collected from each sample and data were analyzed using Genesifter software (formerly Geospiza) (PerkinElmer, Santa Clara CA).
Raw data for each sample were aligned to the most recent mirBASE database (mirBase.org) with remaining reads aligned to the most recent human genome (hg18 build) build in order to identify previously unknown regions that may encode for unique miRNAs.
Pairwise comparison of the alignment results was done using Genesifter for identification of miRNAs that are differentially expressed at a significant level, i.e. up- or down-regulated.
Genome_build: hg18

source_name: HEK293T cells

growth_protocol: The human embryonic kidney cell line containing SV40 T-antigen (HEK293T) was obtained from the American Type Culture Collection (Manassas, VA). HEK293T cells were cultivated in DMEM medium supplemented with 10% exosome-depleted fetal bovine serum (FBS), 100 IU/mL penicillin and 100 μg/mL streptomycin (Corning/Mediatech, Inc. Manassas, VA). Exosome-depleted FBS serum was prepared by pelleting the serum exosomes by ultracentrifugation at 100,000 x g for 2 h at 4°C, and the resulting supernatant was filtered through a 0.2 μm pore filter. Cells were routinely maintained in a humidified chamber at 37°C and 5% CO2.

extract_protocol:
Exosomes were isolated using PEG precipitation protocol according to Rider et al., 2016 (Rider, M. A. et al. ExtraPEG: A Polyethylene Glycol-Based Method for the Enrichment of Extracellular Vesicles. Sci. Rep. 6, 23978; doi: 10.1038/srep23978 (2016)). Collected conditioned cell culture media was clarified by centrifugation at 500x g, 4oC, 11min to remove lose cells and cellular debris) and by second round of centrifugation at 2000x g, 4oC, 30min to remove cellular debris and large apoptotic bodies. Clarified culture supernatants were mixed with an equal volume of 16% PEG6000 in 1M NaCl and rotated at +4oC overnight. Next day, formed precipitates were sedimented at 3665x g, 4oC for 1hr. The precipitate was dissolved in 12ml cold PBS and the exosomes were pelleted at 100,000 x g for 75 min at 4°C. The exosome pellet was washed with 10 ml of 1X PBS and pelleted again by centrifugation at 100,000 x g for 1 h at 4°C. The resulting pellet was either suspended in 1X PBS for whole exosome applications or further processed for RNA or protein extraction. Total RNA was extracted from exosome pellet using Total Exosome RNA & Protein Isolation Kit (Thermo Fisher, Cat#  4478545) following the manufacturer’s protocol. RNA quality and concentration was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Hewlett-Packard Str. 8, 76337 Waldbronn, Germany).
Small RNA libraries were constructed using Illumina TruSeq Small RNA Library Preparation Kit and TruSeq Stranded mRNA kit for Illumina sequencers according to manufacturer’s protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample. Each library was indexed in order to multiplex four samples per sequencing run on the Illumina MiSeq platform using MiSeq 50 cycle Reagent Kits v2.

treatment_protocol: For Nef groups: HEK293T cell cultures were transfected with plasmid containing HIV-1 SF2Nef. mRFP under CMV promoter (kind gift from Dr.Fackler, University Hospital Heidelberg, Germany) using Metafectene (Biontex Laboratories GmbH, Munich, Germany) according to the manufacturer’s protocol. All culture medium containing with non-absorbed transfection material was removed 24 hrs post transfection, cultures were washed 2 times with PBS and fresh DMEM medium supplemented with 10% exosome-depleted fetal bovine serum (FBS), 100 IU/mL penicillin and 100 μg/mL streptomycin was added. Exosome containing (conditioned) culture medium was collected 48 and 72 hrs post transfection. For Mock groups: HEK293T cell cultures were mock transfected using Metafectene (Biontex Laboratories GmbH, Munich, Germany) according to the manufacturer’s protocol using metafectene reagent without any DNA. All culture medium containing with non-absorbed transfection material was removed 24 hrs post transfection, cultures were washed 2 times with PBS and fresh DMEM medium supplemented with 10% exosome-depleted fetal bovine serum (FBS), 100 IU/mL penicillin and 100 μg/mL streptomycin was added. Exosome containing (conditioned) culture medium was collected 48 and 72 hrs post transfection.

tag: cell line

value: kidney

tag: developmental stage

value: embryo

tag: transfection

value: 26Nef transfection


title: 26Nef transfection tp1 [miRNA]

description:
sample that contains small RNAs produced into the culture supernatants in Nef transfection group during the time period between 24 and 48 hrs post-transfection (sample collection were done in January 2018).
26N1
small RNAs


title: Patient 1, cancerous colon tissue, biological replicate 2, technical replicate 2

description:
Patient1_Cancer_bioRep2_techRep2
ColonCancerReplicatesMaster.csv


title: Patient 1, normal colon tissue, biological replicate 1, technical replicate 2

description:
Patient1_Normal_bioRep1_techRep2
ColonCancerReplicatesMaster.csv


title: Liver_Cross-fostered M PND78-86 sample4

description: Biological replicate PND78-86, MM treated

value: MM treated

tag: age


title: Liver_M PND78-86 sample7

description: Biological replicate PND78-86, M control


title: Liver_M PND78-86 sample8


title: Patient 1, normal colon tissue, biological replicate 1, technical replicate 1

description:
Patient1_Normal_bioRep1_techRep1
ColonCancerReplicatesMaster.csv


title: Liver_Cross-fostered control PND21 sample1

description: Biological replicate PND21, CC treated

value: CC treated

value: Postnatal day 21


title: Nef transfection tp1 [miRNA]

description:
sample that contains small RNAs produced into the culture supernatants in Nef transfection group during the time period between 24 and 48 hrs post-transfection (sample collection were done in Novemebr 2017).
N1
small RNAs

value: Nef transfection


title: Mock transfection tp2 [miRNA]

description:
sample that contains small RNAs produced into the culture supernatants in mock transfection group during the time period between 48 and 72 hrs post-transfection (sample collection were done in Novemebr 2017).
M2
small RNAs

value: Mock transfection


title: Nef transfection tp2 [miRNA]

description:
sample that contains small RNAs produced into the culture supernatants in Nef transfection group during the time period between 48 and 72 hrs post-transfection (sample collection were done in Novemebr 2017).
N2
small RNAs


title: Liver_Control PND78-86 sample1

description: Biological replicate PND78-86, control


title: 26Nef transfection tp2

description:
sample that contains exosomes produced into the culture supernatants in Nef transfection group during the time period between 48 and 72 hrs post-transfection (sample collection were done in January 2018).
26N2

data_processing:
Quality trim and filter reads using BBDuk
 Align/map reads to the human genome using STAR
Estimate expression levels using RSEM
Identify differentially expressed genes using edgeR
Genome_build: hg18

extract_protocol:
Exosomes were isolated using PEG precipitation protocol according to Rider et al., 2016 (Rider, M. A. et al. ExtraPEG: A Polyethylene Glycol-Based Method for the Enrichment of Extracellular Vesicles. Sci. Rep. 6, 23978; doi: 10.1038/srep23978 (2016)). Collected conditioned cell culture media was clarified by centrifugation at 500x g, 4oC, 11min to remove lose cells and cellular debris) and by second round of centrifugation at 2000x g, 4oC, 30min to remove cellular debris and large apoptotic bodies. Clarified culture supernatants were mixed with an equal volume of 16% PEG6000 in 1M NaCl and rotated at +4oC overnight. Next day, formed precipitates were sedimented at 3665x g, 4oC for 1hr. The precipitate was dissolved in 12ml cold PBS and the exosomes were pelleted at 100,000 x g for 75 min at 4°C. The exosome pellet was washed with 10 ml of 1X PBS and pelleted again by centrifugation at 100,000 x g for 1 h at 4°C. The resulting pellet was either suspended in 1X PBS for whole exosome applications or further processed for RNA or protein extraction. Total RNA was extracted from exosome pellet using Total Exosome RNA & Protein Isolation Kit (Thermo Fisher, Cat#  4478545) following the manufacturer’s protocol. RNA quality and concentration was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Hewlett-Packard Str. 8, 76337 Waldbronn, Germany).
TruSeq Stranded mRNA kit


title: 26Mock transfection tp2

description:
sample that contains exosomes produced into the culture supernatants in mock transfection group during the time period between 48 and 72 hrs post-transfection (sample collection were done in January 2018).
26M2

value: 26Mock transfection


title: 26Nef transfection tp1

description:
sample that contains exosomes produced into the culture supernatants in Nef transfection group during the time period between 24 and 48 hrs post-transfection (sample collection were done in January 2018).
26N1


title: Nef transfection tp2

description:
sample that contains exosomes produced into the culture supernatants in Nef transfection group during the time period between 48 and 72 hrs post-transfection (sample collection were done in Novemebr 2017).
N2


title: Nef transfection tp1

description:
sample that contains exosomes produced into the culture supernatants in Nef transfection group during the time period between 24 and 48 hrs post-transfection (sample collection were done in Novemebr 2017).
N1


title: Mock transfection tp1

description:
sample that contains exosomes produced into the culture supernatants in mock transfection group during the time period between 24 and 48 hrs post-transfection (sample collection were done in Novemebr 2017).
M1


title: WME226

city: Tianjin

first: Qing

last: Niu

address: No. 288, Nanjing Road, Heping District

institute: Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample

source_name: Bone marrow

extract_protocol:
The frozen bone marrow samples were thawed for cell separation. Cells per sample were counted and stained by antibodies mentioned in Flow cytometric immunophenotyping, and resuspended in 500-1000 µl PBS with 2% fetal bovine serum for sorting with BD AriaⅡ.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.

value: pre-treatment


title: WME611

value: post-treatment


title: Mock transfection tp2

description:
sample that contains exosomes produced into the culture supernatants in mock transfection group during the time period between 48 and 72 hrs post-transfection (sample collection were done in Novemebr 2017).
M2


title: 26Mock transfection tp2 [miRNA]

description:
sample that contains small RNAs produced into the culture supernatants in mock transfection group during the time period between 48 and 72 hrs post-transfection (sample collection were done in January 2018).
26M2
small RNAs


title: SMM4_C92

status: Public on Nov 17 2018

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

data_processing:
Basecalls performed using Illumina bcl2fastq2 versions bcl2fastq-1.8.4 (before therapy) and 2.17.1.14 after therapy)
Sequence reads were aligned to the hg19 genome assembly using TopHat2
Raw and normalized gene counts (RPKM) are generated by Featuregenecounts
Raw gene counts are converted to TPM
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: plasma cells from perpheral blood

extract_protocol: Bone marrow aspirates were collected from 15 patients after informed consent and subjected to ACK lysis and mononuclear cell isolation. Plasma cells were separated by positive selection using CD138 coated magnetic beads (MACS; Miltenyi Biotec, CA) in a RoboSep system (STEMCELL Technology, Canada). CD138 positive cells were examined using Vi-CELL XR (Beckman Coulter, CA) to determine cell number, viability and average size. A microfluidic mRNA-Seq chip (Fluidigm, CA) was used for capturing cells from each sample at a concentration of 500 cells/μl and run in the Fluidigm C1 system to  generate double stranded cDNA using SMARTer Ultra Low RNA kit for Illumina (Takara, CA).  All samples were assessed for cell capture in a C1 chip by direct observation under a microscope and for cDNA quality using Fragment Analyzer (HS Large Fragment kit, Advanced Analytical Technologies, IA).

tag: tumor stage

value: SMM

tag: patient


title: SMM4_C95


title: 26Mock transfection tp1 [miRNA]

description:
sample that contains small RNAs produced into the culture supernatants in mock transfection group during the time period between 24 and 48 hrs post-transfection (sample collection were done in January 2018).
26M1
small RNAs


title: SMM4_C73


title: SMM4_C78


title: SMM4_C71


title: SMM4_C86


title: SMM4_C72


title: SMM4_C90


title: 26Mock transfection tp1

description:
sample that contains exosomes produced into the culture supernatants in mock transfection group during the time period between 24 and 48 hrs post-transfection (sample collection were done in January 2018).
26M1


title: Mock transfection tp1 [miRNA]

description:
sample that contains small RNAs produced into the culture supernatants in mock transfection group during the time period between 24 and 48 hrs post-transfection (sample collection were done in Novemebr 2017).
M1
small RNAs


title: SMM4_C66


title: SMM4_C64


title: SMM4_C68


title: SMM4_C62


title: SMM4_C60


title: SMM4_C63


title: SMM4_C58


title: SMM4_C59


title: SMM4_C54


title: SMM4_C50


title: SMM4_C56


title: SMM4_C51


title: SMM4_C44


title: SMM4_C82


title: SMM4_C80


title: myometrium adiponectin treated vs non-treated 1

city: Olsztyn

first: Kamil

last: Dobrzyn

state: Warminsko-Mazurskie

address: Oczapowskiego, 1A

department: Department of Animal Anatomy and Physiology

country: Poland

institute: University of Warmia and Mazury

hyb_protocol: Two differentially labelled samples (from adiponectin treated and non-treated, control samples) were placed on each array (one slide, n = 4) in a balanced block design with dye swaps. Hybridization was carried out in an Agilent hybridization oven for 17 h at 60°C. After the hybridization process, the microarrays were washed.

scan_protocol: Microarrays were scanned at 5 μm resolution with an Agilent’s High-Resolution C Microarray Scanner according to the manufacturers's protocol.

data_processing: The TIFF image, generated after the scanning process, was used for: data extraction and detailed analysis, background subtraction from features, and dye normalizations (linear and LOWESS); in the Feature Extraction Software. Gene expression data were analysed in GeneSpring GX 12 software (Agilent Technologies, USA) to identify the genes that were differentially expressed in pigs that were and were not treated with adiponectin.

organism: Sus scrofa domesticus

source_name: myometrium non-treated

label_protocol: The RNA isolated from the control and adiponectin treated tissues were labelled with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5), respectively. Quantity and purity of obtained cRNA were measured with NanoQuant plates on the Infinite M200 Pro plate reader . 825 ng of Cy-3 and 825 ng of Cy-5-labeled cRNA were mixed together (for each microarray). According to microarray manufacturer’s protocol, cRNA was fragmented and mixed with hybridization buffer.

growth_protocol: Four mature gilts (Large White x Polish Landrace) were used in the study (n = 4). All individuals were descended from private breeding farm. The gilts were at the age of 7-8 months and the weight of 120 to 130 kg. All animals used in the study were on days 15 to 16 of gestation. The day after coitus was marked as the first day of gestation. Insemination was performed on days 1 to 2 of the oestrous cycle. Pregnancy was confirmed by the presence of conceptuses. 15 to 16 days after coition, gilts were sacrificed. Pigs were slaughtered by qualified abattoir worker.

extract_protocol: Total RNA was extracted from tissues using peqGOLD TriFast isolation system according to the manufacturer’s instructions. RNA purity and quantity were measured spectrophotometrically . RNA quality was checked using RNA 6000 Nano Assay Kit on an Agilent 2100 Bioanalyzer. RNA integrity number (RIN) score between 8 and 10 were used for microarray analysis and quantitative real-time PCR (qPCR) experiments. RNAs were stored at −80 °C until the microarray analysis.

treatment_protocol: The myometrial explants obtained from the middle of uterine horns were cut into small, irregular slices (3 mm of thickness, 100 mg ± 10%). Tissue explants were washed three times in medium M199. The tissue explants were placed in the separate sterile culture vials with 2 mL medium 199. Cultures were preincubated for 2 h (37°C, 95% O2, 5% CO2). To determine the influence of adiponectin on the global gene expression in the myometrium, slices were treated with adiponectin  at the concentration of 10 µg/ml and incubated for another 24 h at the same conditions. Control tissues were incubated without any treatment. All cultures were prepared in duplicates in four separate experiments for each group (n = 4). The myometrial tissue explants were frozen and stored at -80°C for further analyses.

tag: treatment

value: non-treated

tag: period of pregnancy

value: days 15 to 16

tag: race

value: Large White x Polish Landrace

tag: gilts age and weight

value: mature/7-8 months/120 to 130 kg

source_name: myometrium adiponectin-treated

value: adiponectin


title: SMM4_C39


title: SMM4_C41


title: myometrium adiponectin treated vs non-treated 4


title: myometrium adiponectin treated vs non-treated 2


title: SMM4_C38


title: myometrium adiponectin treated vs non-treated 3


title: SMM4_C35


title: SMM4_C24


title: SMM4_C29


title: SMM4_C25


title: SMM4_C26


title: SMM4_C22


title: SMM4_C31


title: SMM4_C34


title: SMM4_C30


title: SMM4_C12


title: SMM4_C17


title: SMM4_C19


title: SMM4_C23


title: SMM4_C08


title: SMM4_C02


title: SMM3_C93


title: SMM3_C88


title: SMM3_C70


title: SMM3_C76


title: SMM3_C67


title: SMM3_C66


title: SMM4_C36


title: SMM3_C63


title: SMM3_C55


title: SMM3_C50


title: SMM4_C33


title: SMM3_C80


title: SMM3_C43


title: SMM4_C04


title: SMM3_C46


title: SMM3_C33


title: SMM3_C44


title: SMM3_C39


title: SMM3_C34


title: SMM3_C40


title: SMM3_C37


title: SMM3_C28


title: SMM3_C25


title: SMM3_C23


title: SMM3_C35


title: SMM3_C32


title: SMM3_C30


title: SMM3_C68


title: SMM3_C24


title: SMM3_C58


title: SMM3_C22


title: SMM3_C14


title: SMM3_C16


title: SMM3_C13


title: SMM3_C05


title: SMM3_C15


title: SMM3_C04


title: SMM3_C10


title: SMM3_C09


title: SMM3_C02


title: SMM3_C49


title: SMM2_C89


title: SMM2_C93


title: SMM2_C52


title: SMM2_C87


title: SMM2_C47


title: SMM2_C27


title: SMM2_C84


title: SMM2_C17


title: SMM2_C25


title: SMM2_C83


title: SMM2_C48


title: SMM2_C19


title: SMM2_C35


title: SMM2_C34


title: SMM0_C91


title: SMM2_C15


title: SMM3_C29


title: SMM0_C89


title: SMM0_C90


title: SMM0_C85


title: SMM0_C87


title: SMM0_C96


title: SMM0_C82


title: SMM0_C95


title: SMM0_C92


title: SMM0_C88


title: SMM0_C86


title: SMM0_C83


title: SMM0_C84


title: SMM0_C80


title: SMM0_C79


title: SMM0_C76


title: SMM0_C78


title: SMM0_C75


title: SMM0_C63


title: SMM0_C74


title: SMM0_C62


title: SMM0_C73


title: SMM0_C72


title: SMM0_C71


title: SMM0_C57


title: SMM0_C58


title: SMM0_C69


title: SMM0_C53


title: SMM0_C67


title: SMM0_C55


title: SMM0_C59


title: SMM0_C56


title: SMM0_C54


title: SMM0_C47


title: SMM0_C49


title: SMM2_C71


title: SMM0_C46


title: SMM0_C45


title: SMM0_C42


title: SMM0_C43


title: SMM0_C51


title: SMM0_C50


title: SMM0_C44


title: SMM0_C40


title: SMM0_C39


title: SMM0_C41


title: SMM0_C33


title: SMM0_C35


title: SMM0_C36


title: SMM0_C29


title: SMM0_C28


title: SMM0_C34


title: SMM0_C37


title: SMM0_C38


title: SMM0_C26


title: SMM0_C19


title: SMM0_C23


title: SMM0_C30


title: SMM0_C24


title: SMM0_C21


title: SMM0_C18


title: SMM0_C52


title: SMM0_C15


title: SMM0_C14


title: SMM0_C12


title: SMM0_C17


title: SMM0_C11


title: SMM0_C10


title: SMM0_C09


title: SMM0_C08


title: SMM0_C05


title: SMM0_C06


title: SMM0_C07


title: SMM0_C04


title: RRMM4_C96

value: RRMM


title: SMM0_C02


title: RRMM4_C93


title: SMM0_C25


title: RRMM4_C81


title: RRMM4_C69


title: RRMM4_C70


title: RRMM4_C72


title: RRMM4_C68


title: RRMM4_C67


title: RRMM4_C56


title: RRMM4_C58


title: RRMM4_C71


title: RRMM4_C59


title: RRMM4_C54


title: RRMM4_C49


title: SMM0_C13


title: RRMM4_C43


title: RRMM4_C35


title: RRMM4_C48


title: SMM0_C03


title: RRMM4_C26


title: RRMM4_C28


title: RRMM4_C21


title: RRMM4_C23


title: RRMM4_C22


title: RRMM4_C89


title: RRMM4_C80


title: RRMM4_C18


title: RRMM4_C15


title: RRMM4_C17


title: RRMM4_C12


title: RRMM4_C10


title: RRMM4_C55


title: RRMM4_C03


title: RRMM4_C02


title: RRMM2_C85


title: RRMM2_C81


title: RRMM2_C84


title: RRMM2_C80


title: RRMM2_C78


title: RRMM2_C77


title: RRMM2_C83


title: RRMM2_C69


title: RRMM2_C75


title: RRMM2_C67


title: RRMM2_C70


title: RRMM2_C72


title: RRMM2_C65


title: RRMM2_C66


title: RRMM2_C68


title: RRMM2_C60


title: RRMM2_C59


title: RRMM2_C58


title: RRMM4_C76


title: RRMM2_C63


title: RRMM2_C57


title: RRMM2_C54


title: RRMM2_C44


title: RRMM2_C52


title: RRMM2_C50


title: RRMM2_C34


title: RRMM2_C32


title: RRMM2_C27


title: RRMM2_C41


title: RRMM2_C21


title: RRMM2_C22


title: RRMM2_C16


title: RRMM2_C18


title: RRMM2_C23


title: RRMM2_C19


title: RRMM2_C05


title: RRMM2_C11


title: RRMM2_C03