title: Patient_1-IL1RAPneg

description: AML cells isolated from patient


title: CHOP_4493_Patient_1

status: Public on Jul 26 2018

type: RNA

city: Los Angeles

first: Daniel

last: Nachun

state: CA

address: 695 Charles E Young Dr S

country: USA

institute: UCLA

hyb_protocol: Total RNA (200 ng) was amplified, biotinylated and hybridized on Illumina HT12 v4 microarrays, as per manufacturer's protocol, at the UCLA Neuroscience Genomics Core (UNGC)

scan_protocol: Slides were scanned using an Illumina BeadStation and signal extracted using the Illumina BeadStudio software

data_processing: Array preprocessing was performed using the standard pipeline from the lumi package which is designed specifically for Illumina microarrays. Raw intensities were normalized using variance-stabilized transformation and interarray normalization was performed with robust spline normalization. Outliers were removed based upon sample-wise connectivity z-scores. Batch effect correction was performed using ComBat from the sva package. Probes were filtered by detection score P < 0.01 and unannotated probes were dropped. Duplicate probes for the same gene were dropped using the maxMean method with the collapseRows function from the WGCNA package, which only keeps probes with the highest mean expression across all of the samples.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: Biotinylation using standard Illumina protocol

extract_protocol: Peripheral blood was collected in Paxgene tubes and frozen before RNA extraction, which was performed using a semi-automated system (Qiacube). RNA quantity was assessed with Nanodrop (Nanodrop Technologies) and quality with the Agilent Bioanalyzer (Agilent Technologies).

tag: pidn

tag: sample number

tag: batch

tag: site

value: CHOP

tag: rin

tag: status

value: Patient

tag: Sex

value: FEMALE

tag: age

tag: onset

tag: duration

tag: functional stage


title: CHOP_4492_Patient_1

value: MALE


title: MCF-7 2D, biological rep1

city: Farmington

first: Nicole

last: Farra

state: Connecticut

address: 263 FARMINGTON AVE

department: Molecular Biology and Biophysics

institute: University of Connecticut Health

description: Gene expression data from MCF-7 monolayer cells harvested at day 3

hyb_protocol: The arrays were hybridized for 16 h at 450° in a rotisserie oven.

scan_protocol: GeneChips were scanned on a Affymetrix GeneChip Scanner 3000.

data_processing: Raw CEL files were checked for quality and RMA normalized using Affymetrix Expression Console Software (version 1.4.1.46).

label: Biotin-labeled

label_protocol: Biotin-labeled cRNA was synthesized from 1 to 5 ug of total RNA by using a one cycle target labeling kit (Affymetrix).

growth_protocol: MCF-7 cells were cultured in Dulbecco’s minimal essential medium (DMEM)–F12 supplemented with 10% FBS and were maintained at 37°C in a humidified atmosphere containing 5% CO2 and 20% O2. To generate spheroids, cells were trypsinized from monolayer cultures and cells were seeded at 8,000 cells/well (8x104 cells/ml) in appropriate plates in corresponding normal growth media. To generate 2D samples, cells were trypsanized and replated at 8x104 cells/ml

extract_protocol: RNA was isolated and purified from cells using High Pure RNA Isolation Kit (Roche Diagnostics) following the manufacturer’s instructions

tag: tissue

value: Breast Epithelial Adenocarcinoma

tag: cell line

tag: culture method

value: 2D monolayer


title: CHOP_4449_Patient_1


title: CHOP_4491_Patient_1


title: CHOP_4446_Patient_1


title: SLR185_5

type: SRA

city: Minneapolis

first: Frank

last: Cichocki

state: MN

address: 420 Delaware Street SE MMC 480

institute: University of Minnesota

library_source: transcriptomic

data_processing:
STAR version 2.4.0d was used to align the RNA sequencing reads to the human genome
The Ensembl gene annotation version 75 was provided as gene transfer format for exon junction support
For each sample reads were assigned to genes and summarized using FeatureCounts (subread package version 1.4.5-p1)
Raw read counds were read into R (v.3.2.0) and subjected to normalization by the trimmed means of M-values normalization method
Differential gene expression was performed using the R/bioconductor package limma
Genome_build: GRCh37 (hg19)

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using the RNAeasy Kit from Qiagen
RNA-seq libraries were generated using the TruSeq RNA Library Prep Kit v2

treatment_protocol: Frozen PBMC aliqouts were thawed and rested overnight in RPMI media with 10% FBS prior to antibody staining and sorting the next day. No cytokines were added

tag: tag

value: FACS sorted

tag: cell type

value: Naive T cells

tag: genotype


title: SLR185_3

value: Late mature canonical NK cells


title: SLR185_4

value: Late mature adaptive NK cells


title: SLR185_6

value: Effector Memory T cells


title: SLR185_2

value: Early mature adaptive NK cells


title: ALLN_siPIWI_2_4_S7_R1_001

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

description: ALLN treated cells (6h) transfected with  siRNA against PIWIL2/PIWIL4

data_processing:
Qiagen’s Geneglobe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances
Supplementary_files_format_and_content: microRNA summary time course
Supplementary_files_format_and_content: microRNA summary PIWIL silencing
Supplementary_files_format_and_content: reads per sample

growth_protocol: Cells were split either into 6-well plates or 10 cm dishes and allowed to grow to 70-80% confluence prior to the start of the experiments.

extract_protocol:
Total RNA containing the microRNA fraction was isolated using miRNeasy kit (Qiagen) according to the manufacturer’s protocol.
MiRNA sequencing libraries were prepared using QIAseq miRNA library kit (Qiagen) following the manufacturer’s instructions and followed by sequencing on an Illumina NextSeq instrument. Using Qiagen’s Geneglobe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances

treatment_protocol: ER stress was induced with ALLN (100uM) and Tunicamycin (2,5 ug/ml) for 2, 6, and 9 hours,

value: normal imortailized human bronchial epithelial cells

tag: passages

tag: agent

value: ALLN

tag: time point

tag: transfection

value: siRNA against PIWIL2/PIWIL4


title: CHOP_4445_Patient_1

tag: pidn

tag: sample number

tag: batch

tag: site

tag: rin


title: TM_siPIWI_2_4_S6_R1_001

description: Tunicamycin treated cells (6h) transfected with  siRNA against PIWIL2/PIWIL3

value: Tunicamycin

value: siRNA against PIWIL2/PIWIL3


title: CHOP_4444_Patient_1

value: CHOP

tag: status

tag: Sex

tag: age

tag: onset

tag: duration


title: CTRL_siPIWI_2_4_S5_R1_001

description: Control cells transfected with cotrol siRNA

value: control siRNA


title: SLR185_1

tag: tag

value: Early mature canonical NK cells


title: CHOP_4443_Patient_1

value: Patient

value: MALE

tag: functional stage


title: RT9_S10_R1_001

description: Cells treated with Tunicamycin for 9h

tag: cell type


title: SLR173_6

tag: genotype


title: SLR173_5


title: CHOP_4442_Patient_1


title: SLR173_4


title: RT2_S7_R1_001

description: Cells treated with Tunicamycin for 2h

tag: passages

tag: agent


title: CHOP_4258_Patient_1

value: FEMALE


title: SLR173_3

value: FACS sorted


title: CHOP_4259_Patient_1


title: RA9_S5_R1_001

description: Cells treated with ALLN for 9h

tag: time point


title: SLR173_2


title: RA6_S4_R1_001

description: Cells treated with ALLN for 6h


title: SLR173_1


title: RA2_S2_R1_001

description: Cells treated with ALLN for 2h


title: SLR117_6


title: SLR117_5

value: Naive T cells


title: RT6_S9_R1_001

description: Cells treated with Tunicamycin for 6h


title: SLR117_4


title: CHOP_4255_Patient_1

tag: pidn


title: Inhibitor replicate 3

city: Bethesda

first: Benjamin

last: Carter

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

data_processing:
Reads were trimmed using Trimmomatic and aligned to the mm10 reference genome using STAR.
Gene expression levels were computed using htseq-count using default parameters.
Differential expression analysis was performed with DESeq2 using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimted text containing the differential expression output from DESeq2.

organism: Mus musculus

growth_protocol: ESCs were cultured in DMEM supplemented with 15% FBS, 1% HEPES, 1% sodium pyruvate, 1% Pen/Strep, 1% glutamine, and 1% nonessential amino acids.

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: developemental stage

value: Embryonic Stem Cells (ESCs)

tag: treatment

value: DMSO solvent + BAF inhibitor


title: Inhibitor replicate 2


title: SLR117_3

value: Late mature canonical NK cells


title: Inhibitor replicate 1


title: CHOP_4254_Patient_1

tag: sample number

tag: batch

tag: site

tag: rin


title: CHOP_4257_Patient_1

tag: status

tag: Sex

tag: age

tag: onset


title: CHOP_4253_Patient_1

tag: duration

tag: functional stage


title: SLR117_2

tag: tag

tag: cell type

value: Early mature adaptive NK cells

tag: genotype


title: CHOP_4246_Patient_1

tag: pidn


title: CHOP_4249_Patient_2


title: RA0_S1_R1_001

description: CONTROL CELLS - NO STRESS

value: normal imortailized human bronchial epithelial cells

tag: passages

tag: agent


title: SLR117_1


title: DMSO replicate 2

tag: strain

tag: developemental stage

tag: treatment

value: DMSO solvent only


title: CHOP_4242_Patient_1

tag: sample number

tag: batch

tag: site


title: DMSO replicate 1


title: SLR037_6

value: Effector Memory T cells


title: CHOP_4241_Patient_1

tag: rin

tag: status

tag: Sex


title: SLR037_5


title: SLR037_4


title: DMSO replicate 3


title: SLR037_3


title: CHOP_4236_Patient_1

tag: age

tag: onset

tag: duration


title: SLR037_2

tag: tag

tag: cell type


title: TGBS_swim-up sperm_rep2

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
Illumina Casava1.4 software used for basecalling.
Targeted methylome sequencing reads were mapped to the mouse reference genome sequence (mm9) using Bmap (http://itolab.med.kyushu-u.ac.jp/BMap/index.html).
Methylation levels were calculated for individual CG sites.
Genome_build: mm9
Supplementary_files_format_and_content: BED files include chrmosome, position, strand, the number of mC reads and the number of total reads.

molecule: genomic DNA

source_name: Spermatozoa

growth_protocol: Caudal epididymis and vas deferens were incubated in M2 medium for 1 hour at 37C to prepare total sperm fraction.

extract_protocol:
After treatment of sperm lysis buffer, genomic DNA was extracted from each sperm sample. DNA is purified by RNase and pronaseK treatment, and extracted by PCI separation and EtOH precipitation.
Libraries for targeted methylome sequencing were prepared according to the post-bisulfite adaptor tagging (PBAT) protocol (Miura F et al., 2012; Miura F and Ito T, 2015) with slight modifications. Briefly, 300 ng of genomic DNA was fragmented to ~500 bp with Covaris S220 and used for target enrichment with SureSelectXT Mouse Methyl-Seq kit (Agilent). The enriched DNA was subjected to PBAT followed by 5 cycles of PCR enrichment with Kapa Library Amplification Kit. Single-read sequencing (100 cycles) was performed on Illumina HiSeq 2500 using HiSeq SR Rapid Cluster Kit v2 and HiSeq Rapid SBS Kit v2. Two indexed libraries were combined with a high concentration of spike-in PhiX control DNA (20%) and loaded on a single lane of the flow cell.
Target BS-seq

treatment_protocol: After mild sonication to separate sperm head from the tail, HRCS (Histone Replacement- Complete Sperm) was isolated from total sperm fraction by 82% Percoll precipitation.

tag: sperm fraction

value: Swim-up sperm

tag: dna selection

value: SureSelect (Agilent)


title: TGBS_HRCS_rep2

value: HRCS


title: CHOP_4235_Patient_1

tag: pidn

value: CHOP

tag: functional stage


title: TGBS_swim-up sperm_rep1

tag: strain


title: SLR037_1

value: Late mature adaptive NK cells

tag: genotype


title: TGBS_HRCS_rep1


title: mTmG;CREERT2_vehicle

city: New York

first: Harold

last: Varmus

state: NY

address: 1300 York Ave

department: Department of Medicine

institute: Weill Cornell Medicine

description:
MEFs underwent two rounds of treatment (vehicle for 24 hr, wash out, and incubated for two more days). U2af1 expression: WT/WT
MEFs_splicing_03202018.xlsx; MEFs_gene_expression_03202018.xlsx

data_processing:
Analysis of mRNA sequencing samples was the same as our previous submission (GEO: GSE80136). Briefly, reads were first mapped to these transcripts using RSEM [PMCID: PMC3163565]. Remaining unaligned reads were then mapped to a database of possible junctions between all 5' and 3' splice sites of those transcripts, and then subsequently to the GRCm38 mouse genome assembly, using TopHat [PMID: 19289445]. These read counts were then subjected to Wagenmakers’s Bayesian alternative to the binomial proportion test [PMID: 20064637]. Differentially spliced events were defined as those that exhibited a difference in absolute isoform ratio of at least 10%; differentially expressed genes (coding) were defined as those that exhibited at lease two-fold difference in a group comparison as indicated.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel tables. In the table for altered splicing events, each row corresponds to an isoform of a splicing event that is differentially spliced for the indicated comparisons that do or do not express U2af1(S34F). In each case, the isoform for which information is given is as follows: the inclusion isoform for cassette exons (type “se”), the intron-proximal isoform for competing 5' or 3' splice site events (types “a5ss” or “a3ss”), inclusion of the upstream exon for mutually exclusive exon events (type “mxe”), splicing of retained introns annotated as alternative (type “ri”) or constitutive (type “ci”), or canonical splicing of an annotated constitutive junction (type “cj”). The columns specify relevant annotations for each event as follows: “coords” specifies the genomic coordinates of the event; “gene” specifies the Ensembl gene ID; “geneName” specifies the gene name; “geneDescription” is a description of the gene as given by Ensembl; “type” specifies the type of splicing event; “nmdTarget” specifies whether the isoform is a predicted substrate for degradation by NMD (NA indicates that either all or no isoforms of the event are predicted NMD substrates). The columns prefixed by “deltaPsi_” give the absolute difference in isoform ratio (Percent Spliced In or “PSI” value) for the indicated comparisons. In the table for altered gene expression, each row corresponds to a coding gene that is differentially expressed for the indicated comparisons that do or do not express U2af1(S34F). Only those with at least 2-fold difference (logFoldChange ≥ 1 or ≤ -1) and p value (pval ≤ 0.05) were shown.

source_name: MEFs treated with vehicle (ethanol)

growth_protocol: MEFs were cultured in DMEM, supplemented with 10% fetal bovine serum and Penicillin-Streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) or AllPrep DNA/RNA kit (Qiagen)
TruSeq RNA Sample Preparation (Non-Stranded and Poly-A selection) for mRNA sequencing

treatment_protocol: MEFs were treated with 4OHT (500 ng/ml) or vehicle for 24 hr, incubate for 48 hr without the drug, repeat the 4OHT (500 ng/ml) or vehicle treatment for 24 hr, and incubate for another 48 hr without the drug before harvest for RNA. Mice were treated with poly (IC). Lineage-cKit+ (Lin-cKit+) cells were isolated from mouse bone marrow 4 weeks later by fluorescence-activated cell sorting (FACS). In another set of experiments, end-stage mice, which were either treated with poly (IC) and ENU or were the splenic recipients of such mice, were used for isoloation of Lin-cKit+ cells by FACS.

tag: treatment

value: vehicle

value: mTmG/WT; UBC-CREERT2/WT


title: CHOP_4234_Patient_1

tag: sample number

tag: batch

value: Patient

value: FEMALE


title: CHOP_4233_Patient_1

tag: site

tag: rin

value: MALE


title: HPBMC_6

value: FACS sorted


title: MGS34F;CREERT2_vehicle

value: MGS34F/WT; GFP/WT; UBC-CREERT2/WT


title: CHOP_4230_Patient_1

tag: status

tag: Sex


title: IES34F;CREERT2_vehicle

value: IES34F/WT; GFP/WT; UBC-CREERT2/WT


title: HPBMC_4

value: Early mature canonical NK cells


title: CHOP_4232_Patient_2

tag: age

tag: onset


title: H9-rNSC-Rep2

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: H9-hESC derived rosette-type Neural Stem Cells

growth_protocol: H9-hESCs and iPSCs were grown in E8 medium

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen), and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample prep kit

treatment_protocol: Basal medium was used to make pNSC, rNSC, IPC, and GPLC consisting of DMEM/F12 supplemented with 543μg/ml Sodium bicarbonate (sigma-aldrich), 1X B-27 Supplement without vitamin A (Thermo Fisher Scientific), 1X N-2 Supplement (Thermo Fisher Scientific), 1% penicillin-streptomycin (Thermo Fisher Scientific). 1% L-glutamine (Thermo Fisher Scientific), 1% non-essential amino acids (Thermo Fisher Scientific). To differentiate into primitive NSCs (pNSCs), medium was replaced into LSC medium containing 10ng/ml LIF (Leukemia Inhibitory Factor, Millipore), 2μM SB431542 (Tocris), and 3μM Chir99021 (Tocris) for 2 weeks. To induce ventral rosette type NSCs, pNSCs were cultured in FEP medium consisting of Basal medium supplemented with 20ng/ml FGF2 (Peprotech), 20ng/ml EGF (Peprotech), 0.5μM Purmorphamine (Tocris).

value: rosette-type Neural Stem Cells


title: H9-hESC-Rep3

source_name: human Embryonic Stem Cells (H9)

value: Embryonic Stem Cells


title: HPBMC_3

tag: tag

value: Early mature adaptive NK cells


title: CHOP_4226_Patient_2

tag: duration


title: MGS34F;CREERT2_4OHT

description:
MEFs underwent two rounds of treatment (4OHT for 24 hr, wash out, and incubated for two more days). U2af1 expression: S34F/WT
MEFs_splicing_03202018.xlsx; MEFs_gene_expression_03202018.xlsx

source_name: MEFs treated with 4OHT

value: 4OHT (500 ng/ml)


title: HPBMC_1

tag: cell type


title: CHOP_4229_Patient_1


title: H9-pNSC-Rep1

source_name: H9-hESC derived primitive Neural Stem Cells

value: primitive Neural Stem Cells


title: HPBMC_2

value: Late mature canonical NK cells


title: HPBMC_5

value: Naive T cells


title: CHOP_4224_Patient_1

value: CHOP


title: H3K27ac ChIP-seq DIO Liver ZT22

city: Houston

first: Dongyin

last: Guan

state: TX

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie version 1.1.1 (Langmead et al., 2009) with parameters  -n 1 -m 1 . Only one uniquely aligning read per genomic position was kept for further analysis. Peak calling was performed with HOMER (Heinz et al., 2010)
Genome_build: mm9
Supplementary_files_format_and_content: UCSC genome browser tracks (bigwig files) and ChIP-seq peak calls (bedgraph files) were generated by HOMER.

source_name: Liver

extract_protocol:
ChIP assays were carried out as described previously (Zhang et al., 2015).  Briefly, mouse livers were harvested, minced, and cross-linked in 1% formaldehyde for 20 min followed by quenching with 1/20 volume of 2.5 M glycine solution for 5 min and two washes with 1  PBS. Chromatin fragmentation was performed by sonication in lysis buffer (50 mM Tris-HCL at pH 8.0, 0.1%SDS, 10 mM EDTA) using the Bioruptor (Diagenode). Proteins were immunoprecipitated in ChIP buffer using anti-H3K27ac overnight. Cross-linking was reversed overnight at 65 C in SDS buffer (50 mM Tris-HCL, 10 mM EDTA, 1% SDS at pH 8), and DNA was isolated using phenol/chloroform/isoamyl alcohol. Precipitated DNA was analyzed by qPCR or high-throughput sequencing.
DNA was amplified according to the ChIP-seq sample preparation guide provided by Illumina using adaptor oligo and primers from Illumina, enzymes from New England Biolabs, and PCR purification kit and MinElute kit from Qiagen. All ChIP-seq libraries were sequenced on Hiseq 2500 (single-end 50bp) by the Functional Genomics Core of the Penn Diabetes Research Center.

tag: tissue

value: liver

tag: diet

value: DIO (Research Diet D12492)

tag: antibody

tag: time


title: GRO-seq DIO Liver ZT22

data_processing:
Library strategy: GRO-seq
PolyA tail was trimmed off each sequencing read. Reads longer than 20bp were then mapped to the mouse genome (mm9) using Bowtie v0.12.8 (Langmead et al., 2009) with parameters ‘-n 1 -l 20 -m 1 –f’. Uniquely mapped reads were extended to 150bp in the 5’ to 3’ direction and used for downstream analysis. Bigwig files were generated using HOMER v4.3 (Heinz et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: UCSC genome browser tracks (bigwig files) and ChIP-seq peak calls (bedgraph files) were generated by HOMER.

extract_protocol:
Mouse liver was harvested at indicated time and washed with cold swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 2 U/ml Superase-In). Nuclear extract was prepared by dounce homogenization in cold swelling buffer and filtered using the cell strainer (100 µm, BD Biosciences). Lysate was centrifuged at 400g for 10 min, then resuspended in lysis buffer (swelling buffer with 10% glycerol and 1% Igepal) and incubated on ice for 5 min. Nuclei were washed twice with lysis buffer, and resuspended at the concentration of 10 x 10-7 nuclei/ ml in freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA).
The nuclear run-on assay was performed as previously described (Core et al., 2008; Step, 2014; Wang et al., 2011). Synthesis of cDNA from RNA was performed as described previously (Wang et al., 2011). cDNA was denatured at 70°C for 3 min then products from 105-400 nucleotides size were excised and eluted from shredded gel pieces for 4h in TE + 0.1% Tween and precipitated by adding 1 µl of glycogen, 300 mM NaCl and 2 volumes of ethanol and incubated overnight at -20°C. cDNA was resuspended into circularization reaction and circularized with CircLigase (Epicentre) for 1 hour at 60°C, denatured for 10 min at 80°C, and relinearized by adding relinearization mix (25 mM KCl, 500 µM DTT) and APE I (15U; New England Biolabs). Linearized DNA was amplified by PCR using Phusion Hot Start II Kit. The PCR product from 150-305 nucleotides size were eluted from shredded gel pieces and purified using ChIP DNA Clean and Concentrator Kit (Genesee Scientific).

tag: strain


title: mTmG;CREERT2_4OHT

description:
MEFs underwent two rounds of treatment (4OHT for 24 hr, wash out, and incubated for two more days). U2af1 expression: WT/WT
MEFs_splicing_03202018.xlsx; MEFs_gene_expression_03202018.xlsx

tag: treatment

tag: genotype

value: mTmG/WT; UBC-CREERT2/WT


title: CHOP_4228_Patient_1

tag: pidn

tag: sample number

tag: batch

value: Patient

value: FEMALE

tag: functional stage


title: GRO-seq DIO Liver ZT19


title: IES34F;CREERT2_4OHT


title: GRO-seq DIO Liver ZT16


title: DK_S23

city: Durham

first: Liuyang

last: Wang

state: NC

address: 0049 CARL Building

institute: Duke University

description: RNAseq for siRNA of ZBTB20 gene at 48h

data_processing:
RNA-seq data were processed using the TrimGalore toolkit (Krueger, 2017), which employs Cutadapt (Martin, 2011) to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer were kept for further analysis. Reads were mapped to the GrCh37v75 version of the human genome and transcriptome (Kersey et al., 2012) using the STAR RNA-seq alignment tool (Dobin et al., 2013).
Reads were kept for subsequent analysis if they mapped to a single genomic location. Gene counts were compiled using the HTSeq tool (Anders et al., 2015). Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 (Love et al., 2014)
Genome_build: GRCH37v75
Supplementary_files_format_and_content: tab-delimited text files include normalized abundances measurements by DESeq2 for each sample

extract_protocol:
RNA was harvested 24 hours and 48 hours post infection with RNAprotect and RNeasy Plus kit (Qiagen)
Library preparation was performed using Illumina TruSeq Stranded RNA-Seq kit by the Duke University Sequencing and Genomic Technologies Core Facility.

value: liver tumor

tag: cell line

tag: sirna

value: siRNA of ZBTB20

value: 48 hours


title: DK_S19

description: RNAseq for siRNA of ZBTB20 gene at 48h


title: DK_S21

description: non-targeting RNAseq at 48h

value: non-targeting


title: DK_S15

description: RNAseq for siRNA of ZBTB20 gene at 48h


title: DK_S17

description: non-targeting RNAseq at 48h


title: CHOP_4227_Patient_1

tag: site

tag: rin

tag: status

tag: Sex

tag: age

tag: onset


title: H3K27ac ChIP-seq DIO Liver ZT10

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie version 1.1.1 (Langmead et al., 2009) with parameters  -n 1 -m 1 . Only one uniquely aligning read per genomic position was kept for further analysis. Peak calling was performed with HOMER (Heinz et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: UCSC genome browser tracks (bigwig files) and ChIP-seq peak calls (bedgraph files) were generated by HOMER.

tag: tissue

tag: diet

tag: antibody


title: CHOP_4199_Patient_1

tag: duration


title: DK_S11

description: RNAseq for siRNA of ZBTB20 gene at 24h

tag: cell type

tag: time

value: 24 hours


title: CHOP_4222_Patient_1

tag: pidn

tag: sample number


title: CHOP_4198_Patient_1

tag: batch

tag: functional stage


title: GRO-seq DIO Liver ZT7

tag: strain


title: GRO-seq DIO Liver ZT10


title: CHOP_4196_Patient_1

tag: site

value: MALE


title: CHOP_4195_Patient_1

tag: rin


title: CHOP_4200_Patient_1

tag: status


title: DK_S13

description: non-targeting RNAseq at 48h

tag: cell line

tag: sirna


title: CHOP_4221_Patient_1

tag: Sex

tag: age

tag: onset


title: DK_S7

description: RNAseq for siRNA of ZBTB20 gene at 24h


title: DK_S5

description: non-targeting RNAseq at 24h


title: DK_S9

description: non-targeting RNAseq at 24h


title: GRO-seq DIO Liver ZT13

tag: tissue

tag: diet

tag: antibody


title: DK_S1

description: non-targeting RNAseq at 24h

tag: cell type

tag: time


title: CHOP_4192_Patient_1

tag: pidn

tag: sample number

tag: duration


title: Undifferentiated cells Rep 2

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Single cell (sc) RNA-seq processing was performed with Cell Ranger software (10x Genomics, Inc.). scRNA-seq samples were demultiplexed with cellranger mkfastq. The annotation file was modified to count reads assigned to both GFP and mCherry cassettes and UMIs counted with cellranger count. Sequencing reads were aligned to a custom mouse genome.
Libraries from both samples were aggregated and normalised by depth, to have the same of number of mapped reads, with cellranger aggr.
Genome_build: Cell Ranger mm10 version 1.2.0 including GFP and mCherry sequences as extra chromosomes
Supplementary_files_format_and_content: Gene expression matrix, containing both cell and expression details, were processed for downstream analysis using cellRanger’s load_cellranger_matrix.

source_name: Adult mouse undifferentiated spermatogonia

growth_protocol: Adult transgenic mice (6-8 weeks old) containing the Plzf-mCherry/CreER reporter were maintained under standard conditions. Mice also carried an Oct4-GFP transgene although this reporter was not used for cell isolation. Mouse background was mixed CBA/C57BL6.

extract_protocol:
Sorted cells were resuspended at ~300 viable cells/μl in PBS containing 0.04% BSA prior to RNA extraction and library preperation using the 10x Chromium system.
Library construction was performed using a 10X Chromium controller with the Chromium Single Cell 3’ Reagent Kit V2. Both libraries were sequenced in one high-output lane of an Illumina NextSeq in single-read 150b format (115b effective read length)

treatment_protocol: Testis cell suspensions were prepared by a standard two step digestion protocol with collagenase and trypsin. Cells were sorted on a BD Influx Cell Sorter (BD Biosciences). The undifferentiated population was gated according to expression of the Plzf-mCherry/CreER reporter plus surface markers c-KIT and CD9. PLZF is a well-established marker of undifferentiated spermatogonia plus cells at early differentiation stages. c-KIT marks differentiating spermatogonia and CD9 is enriched on functional stem cells.

value: spermatogonia

tag: genotype/variation

value: transgenic containing the Plzf-mCherry/CreER reporter

value: adult; 6-8 weeks old

value: Testis


title: CHOP_4186_Patient_1

tag: batch

tag: site

tag: functional stage


title: Undifferentiated cells Rep 1


title: CHOP_4188_Patient_1

tag: rin

tag: status


title: CHOP_4117_Patient_1

tag: Sex


title: CHOP_4183_Patient_1

tag: age


title: CHOP_4182_Patient_1

tag: onset


title: aP_PT_TCM (62)

city: La Jolla

first: Mariana

last: Babor

address: 9420 Athena Cir

institute: La Jolla Institute for Allergy and Immunology

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as matrix tables

molecule: polyA RNA

source_name: aP, cells Pertussis-specific, TCM

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stimulated with peptides in a 24h AIM assay (Dan et al. 2016), stained with antibodies, and an average of 10,000 antigen-specfic cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol.  TCM and TEM were defined as the combination of CCR7+CD45RA- or CCR7-CD45RA- populations respectively. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the (microscaled) smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

tag: individual id

tag: disease group

value: San Diego acellular Pertussis (aP) vaccine

value: Cryopreserved PBMC

tag: stimulation

value: PT

tag: cell subset

value: TCM CD3+CD4+CCR7+CD45RA- T cells


title: aP_TT_TCM (64)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

source_name: aP, cells Tetanus-specific, TCM

tag: cell type

value: TT


title: aP_PT_TEM (61)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

source_name: aP, cells Pertussis-specific, TEM

value: TEM CD3+CD4+CCR7-CD45RA- T cells


title: aP_TT_TEM (59)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

source_name: aP, cells Tetanus-specific, TEM


title: DK_S3

description: RNAseq for siRNA of ZBTB20 gene at 24h

tag: cell line

tag: sirna

tag: time


title: aP_PT_TCM (58)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_PT_TEM (57)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: UCLA_4095_Patient_1

tag: pidn

tag: sample number

value: UCLA

value: Patient

value: FEMALE

tag: duration


title: CHOP_4185_Patient_1

tag: batch

tag: site

value: CHOP

tag: functional stage


title: CHOP_4194_Patient_1

tag: rin

tag: status

tag: Sex


title: CHOP_4181_Patient_1

tag: age

tag: onset


title: GRO-seq DIO Liver ZT1

tag: tissue

value: liver

tag: strain

tag: diet

value: DIO (Research Diet D12492)

tag: antibody


title: CHOP_4111_Patient_2


title: CHOP_4184_Patient_1r

value: MALE


title: UCLA_4086_Patient_1


title: CHOP_4090_Patient_1


title: aP_TT_TEM (63)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: individual id

tag: disease group

tag: cell type

tag: stimulation

tag: cell subset


title: aP_TT_TCM (60)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: CHOP_4080_Patient_1

tag: pidn

tag: sample number

tag: batch

tag: duration


title: aP_TT_TEM (55)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: CHOP_4077_Patient_1

tag: site

tag: rin

tag: status

tag: functional stage


title: aP_PT_TCM (54)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_PT_TEM (53)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_PT_TCM (50)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_TT_TEM (51)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_TT_TCM (56)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_PT_TEM (49)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_PT_TCM (46)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_PT_TEM (45)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_TT_TEM (47)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_TT_TCM (44)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_TT_TCM (48)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: CHOP_4075_Patient_1

tag: Sex

tag: age

tag: onset


title: CHOP_4074_Patient_1


title: CHOP_4076_Patient_1


title: CHOP_4069_Patient_1


title: CHOP_4043_Patient_1


title: CHOP_4041_Patient_1


title: aP_TT_TCM (52)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: aP_TT_TEM (43)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: CHOP_4030_Patient_1


title: Adult Clone 3_miRNA_ISS-cultured

city: Loma Linda

first: Jonathan

last: Baio

address: 24941 Stewart St, Room 326

department: Pathology and Human Anatomy

institute: Loma Linda University School of Medicine

description:
ISS-cultured
SAMPLE 12

data_processing:
Normalization and comparative Ct method analysis per clone was perofmred using Qiagen's web-based software package: http://www.qiagen.com/ us/shop/genes-and-pathways/data-analysis-center-overview-page/
For normalization, we used the average of all available housekeeping genes included on the microarray plates
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
Fold changes per clone were exported to Prism for subsequent analysis. Fold Change worksheet reports test/control (i.e., ISS-cultured CPCs/ground CPCs) ratios.

label: SYBR Green

source_name: Primary cardiac tissue

label_protocol: PCR assays were performed using human development and differentiation microarray plates (MIHS-103ZA; Qiagen, Valencia, CA) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the miScript SYBR Green PCR master mix  and 10X universal primer mix (Qiagen, Valencia, CA). Quantitative real-time PCR were performed (iQ5 thermal cycler, BioRad) with 40 cycles at 94 oC for 15 seconds, 55 oC for 30 secons, and 70 oC for 30 seconds.

growth_protocol: CPCs were flown to the ISS where they were cultured for 12 days and fixed in RNA protect. Clone-, patient-, and passage-matched controls were seeded and grown on the ground for 12 days as a control.

extract_protocol: Total RNA was extracted using TRIzol and alcohol-based precipitation

value: Cardiovascular progenitor cell

tag: culture condition

value: Biocell (BioServe Space Technologies) - ISS

value: 12 days


title: CHOP_4066_Patient_1


title: Adult Clone 3_miRNA_ground_control

description:
Ground control
SAMPLE 11

value: Biocell (BioServe Space Technologies) - Ground


title: CHOP_4065_Patient_2


title: CHOP_4070_Patient_2


title: CHOP_4032_Patient_2


title: CHOP_4028_Patient_1


title: CHOP_4042_Patient_1


title: aP_PT_TCM (42)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: individual id

value: San Diego acellular Pertussis (aP) vaccine


title: CHOP_282_Patient_1


title: aP_TT_TCM (40)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: disease group

value: Cryopreserved PBMC


title: aP_PT_TEM (41)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: cell type

value: PT


title: Adult Clone 1_miRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 8


title: aP_TT_TEM (39)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: stimulation


title: Adult Clone 1_miRNA_ground_control

description:
Ground control
SAMPLE 7


title: CHOP_272_Patient_1


title: aP_PT_TCM (38)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: cell subset

value: TCM CD3+CD4+CCR7+CD45RA- T cells


title: Neonatal Clone 3_miRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 6


title: aP_PT_TEM (37)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: Neonatal Clone 3_miRNA_ground_control

description:
Ground control
SAMPLE 5


title: Adult Clone 2_miRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 10


title: Neonatal Clone 2_miRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 4


title: CHOP_278_Patient_1

tag: pidn


title: Neonatal Clone 2_miRNA_ground_control

description:
Ground control
SAMPLE 3


title: CHOP_276_Patient_1

tag: sample number


title: Adult Clone 2_miRNA_ground_control

description:
Ground control
SAMPLE 9


title: CHOP_249_Patient_1

tag: batch


title: CHOP_254_Patient_1

tag: duration


title: aP_TT_TEM (35)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

value: TT


title: CHOP_281_Patient_1

tag: site


title: aP_PT_TCM (34)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: Neonatal Clone 1_miRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 2


title: CHOP_253_Patient_1

tag: rin


title: Neonatal Clone 1_miRNA_ground_control

description:
Ground control
SAMPLE 1


title: aP_PT_TEM (33)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

value: TEM CD3+CD4+CCR7-CD45RA- T cells


title: CHOP_245_Patient_1

tag: status


title: CHOP_244_Patient_1


title: aP_TT_TCM (36)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: CHOP_242_Patient_1

tag: functional stage


title: Adult Clone 3_mRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 12

data_processing:
Normalization and comparative Ct method analysis per clone was performed using Qiagen's web-based software package: http://www.qiagen.com/ us/shop/genes-and-pathways/data-analysis-center-overview-page/
For normalization, we used the average of GAPDH and ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
Fold changes per clone were exported to Prism for subsequent analysis. Fold Change worksheet reports test/control (i.e., ISS-cultured CPCs/ground CPCs) ratios.

label_protocol: PCR assays were performed using custom designed array plates (Qiagen, Valencia, CA) following the Manufacturer’s instructions. Reverse transcription was performed from 2000 ng total RNA using the Superscript III kit (Life Technologies, Carlsbad, CA). Quantitative real-time PCR were performed (iQ5 thermal cycler, BioRad) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit or using TRIzol and alcohol-based precipitation


title: wP_TT_TCM (32)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

source_name: wP, cells Tetanus-specific, TCM

value: San Diego whole Pertussis (wP) Vaccine


title: wP_TT_TEM (31)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

source_name: wP, cells Tetanus-specific, TEM


title: Adult Clone 3_mRNA_ground_control

description:
Ground control
SAMPLE 11


title: wP_PT_TCM (30)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

source_name: wP, cells Pertussis-specific, TCM


title: UCLA_241_Patient_1

source_name: Whole blood

value: UCLA

value: Patient

tag: Sex


title: Adult Clone 2_mRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 10


title: CHOP_239_Patient_1

value: CHOP

tag: age


title: wP_TT_TCM (28)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: wP_TT_TEM (27)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: Adult Clone 1_mRNA_ground_control

description:
Ground control
SAMPLE 7


title: Adult Clone 2_mRNA_ground_control

description:
Ground control
SAMPLE 9


title: Adult Clone 1_mRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 8


title: Neonatal Clone 3_mRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 6


title: CHOP_237_Patient_1

tag: onset


title: wP_PT_TCM (26)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: Neonatal Clone 2_mRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 4

tag: culture condition


title: wP_TT_TCM (24)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: individual id


title: wP_PT_TEM (25)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

source_name: wP, cells Pertussis-specific, TEM

tag: disease group


title: Neonatal Clone 3_mRNA_ground_control

description:
Ground control
SAMPLE 5

tag: cell type


title: wP_PT_TEM (29)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: stimulation


title: wP_TT_TEM (23)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: cell subset


title: CHOP_233_Patient_1

tag: pidn

value: FEMALE


title: CHOP_216_Patient_1r

tag: sample number


title: Neonatal Clone 2_mRNA_ground_control

description:
Ground control
SAMPLE 3


title: Neonatal Clone 1_mRNA_ISS-cultured

description:
ISS-cultured
SAMPLE 2


title: CHOP_230_Patient_1

tag: batch


title: UCLA_214_Patient_1

tag: duration


title: CHOP_231_Patient_1

tag: site


title: wP_PT_TCM (22)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: Adult Clone 3_conventionalRT-PCR_ISS-cultured

description: ISS-cultured

label_protocol:
mRNA: PCR assays for genes were performed using individual primer pairs (ID_REF A01-B04), cDNA prepared as described, and SYBR Green Master Mix (Promega, Madison, WI).  Reverse transcription was performed from 2000 ng total RNA using the Superscript III kit (Life Technologies, Carlsbad, CA). Quantitative real-time PCR were performed (iQ5 thermal cycler, BioRad) with 45 cycles at 95 oC for 15 seconds, 57 oC for 60 seconds, and 72 oC for 30 seconds (with the exception of YAP1, which was run at 45 cycles at 95 oC for 15 seconds, 55 oC for 60 seconds, and 72 oC for 30 seconds).
microRNA: PCR assays for microRNA gene expression were performed using individual primer pairs (ID_REF B05-B08) , cDNA prepared as described, and QuantiText SYBR Green PCR Master Mix (Qiagen, Valencia, CA). Reverse transcription was performed from 500 ng total RNA using the miScript SYBR Green PCR master mix  and 10X universal primer mix (Qiagen, Valencia, CA). Quantitative real-time PCR were performed (iQ5 thermal cycler, BioRad) with 40 cycles at 94 oC for 15 seconds, 55 oC for 30 secons, and 70 oC for 30 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit or using TRIzol (for microRNA) and alcohol-based precipitation


title: Adult Clone 3_conventionalRT-PCR_ground_control

description: Ground control


title: Neonatal Clone 1_mRNA_ground_control

description:
Ground control
SAMPLE 1


title: wP_PT_TEM (21)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: Adult Clone 2_conventionalRT-PCR_ISS-cultured

description: ISS-cultured


title: CHOP_196_Patient_1

tag: rin


title: wP_TT_TEM (19)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: wP_TT_TCM (20)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: UCLA_210_Patient_1

tag: status


title: UCLA_209_Patient_1

tag: functional stage


title: CHOP_203_Patient_1

tag: Sex


title: GRO-seq DIO Liver ZT4

tag: tissue

value: liver

tag: strain

tag: diet

value: DIO (Research Diet D12492)

tag: antibody

tag: time


title: wP_PT_TCM (18)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: individual id

tag: disease group

tag: cell type


title: Adult Clone 1_conventionalRT-PCR_ISS-cultured

description: ISS-cultured

value: Cardiovascular progenitor cell

tag: culture condition


title: UCLA_191_Patient_1

tag: pidn

tag: sample number

tag: age

tag: onset


title: wP_TT_TCM (16)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: stimulation

tag: cell subset


title: Adult Clone 1_conventionalRT-PCR_ground_control

description: Ground control

tag: duration


title: wP_TT_TEM (15)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: Neonatal Clone 3_conventionalRT-PCR_ground_control

description: Ground control


title: CHOP_188_Patient_1

tag: batch

tag: site

tag: rin

tag: status

tag: Sex

value: MALE

tag: functional stage


title: CHOP_182_Patient_1


title: Neonatal Clone 2_conventionalRT-PCR_ISS-cultured

description: ISS-cultured

value: Biocell (BioServe Space Technologies) - ISS

value: 12 days


title: wP_PT_TEM (13)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: individual id


title: CHOP_185_Patient_1


title: wP_PT_TCM (14)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: disease group


title: Neonatal Clone 2_conventionalRT-PCR_ground_control

description: Ground control

tag: cell type

value: Biocell (BioServe Space Technologies) - Ground


title: Neonatal Clone 1_conventionalRT-PCR_ISS-cultured

description: ISS-cultured

tag: culture condition


title: wP_PT_TEM (17)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

value: Cryopreserved PBMC


title: wP_TT_TEM (11)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: Adult Clone 2_conventionalRT-PCR_ground_control

description: Ground control


title: Neonatal Clone 1_conventionalRT-PCR_ground_control

description: Ground control


title: UCLA_169_Patient_1

tag: pidn


title: Neonatal Clone 3_conventionalRT-PCR_ISS-cultured

description: ISS-cultured


title: wP_PT_TCM (10)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

value: PT


title: CHOP_180_Patient_1

tag: sample number


title: CHOP_194_Patient_1

tag: age


title: wP_TT_TCM (12)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

value: TCM CD3+CD4+CCR7+CD45RA- T cells


title: wP_PT_TEM (9)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: UCLA_171_Patient_1

tag: onset


title: CHOP_162_Patient_1


title: wP_TT_TCM (8)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: stimulation

value: TT


title: UCLA_163_Patient_1


title: wP_TT_TEM (7)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

tag: cell subset

value: TEM CD3+CD4+CCR7-CD45RA- T cells


title: CHOP_161_Patient_1

tag: duration


title: M2 CM treated A549

city: Taipei

first: Chih-Chan

last: Lee

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: Molecular medicine program

description: 2 days treatment

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE 8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: M2 macrophage conditioned media

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: cultivated in RPMI + 5% fetal bovine serum

extract_protocol: Total RNA were extracted by RNeasy mini kit (Cat. 74106; Qiagen, Hilden, Germany), and 100 ng to 1 ug of total RNA were subjected into reverse transcription using the SuperScriptTM III Reverse transcriptase kit (Invitrogen) as directed by the manufacturer.

treatment_protocol: A549 cells were treated with M0, M1, and M2 conditioned media.

tag: cell line

value: lung cancer


title: wP_PT_TCM (6)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv

value: San Diego whole Pertussis (wP) Vaccine


title: wP_PT_TEM (5)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: wP_TT_TCM (4)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: wP_TT_TEM (3)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: wP_PT_TCM (2)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: wP_PT_TEM (1)

description:
PT_all_TPM.tsv
PT_all_TPM.tsv


title: M0 CM treated A549

description: 2 days treatment

source_name: M0 macrophage conditioned media


title: EXP_REP2.fastq.gz

city: waltham

first: weifei

last: luo

state: MA

address: 415 South st

department: Department of Biology

institute: Brandeis University

data_processing:
RNA sequencing data were analyzed as described in (Rodriguez et al., 2012; McMahon et al., 2016)
Scripts available on GitHub (https://github.com/rosbashlab/TRIBE).
Alignment to dm3 genome was done with Tophat v2.1.1 with referenence annotation in gtf format. Multimapped reads are removed.
Genome_build: Release 5/dm3
Supplementary_files_format_and_content: RNA editing sites are provided in bedgraph file format

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
Nascent RNAs were prepared acoording to Khodor et al 2011.
RNA-seq libraries were prepared using illumina Truseq kits.

treatment_protocol: NonA-ADAR funsion protein expression in neurons was induced by RU486.

tag: tribe expression

value: induced

tag: rna

value: nascent RNA

tag: sample type

value: experiment


title: EXP_REP1.fastq.gz


title: EXP_REP3.fastq.gz


title: CHOP_156_Patient_1

data_processing: Array preprocessing was performed using the standard pipeline from the lumi package which is designed specifically for Illumina microarrays. Raw intensities were normalized using variance-stabilized transformation and interarray normalization was performed with robust spline normalization. Outliers were removed based upon sample-wise connectivity z-scores. Batch effect correction was performed using ComBat from the sva package. Probes were filtered by detection score P < 0.01 and unannotated probes were dropped. Duplicate probes for the same gene were dropped using the maxMean method with the collapseRows function from the WGCNA package, which only keeps probes with the highest mean expression across all of the samples.

extract_protocol: Peripheral blood was collected in Paxgene tubes and frozen before RNA extraction, which was performed using a semi-automated system (Qiacube). RNA quantity was assessed with Nanodrop (Nanodrop Technologies) and quality with the Agilent Bioanalyzer (Agilent Technologies).

tag: batch

tag: site

value: CHOP

tag: rin

tag: status

value: Patient

tag: Sex


title: CHOP_145_Patient_1

value: FEMALE


title: UCLA_157_Patient_1

value: UCLA

value: MALE

tag: functional stage


title: CHOP_146_Patient_1

tag: pidn


title: CHOP_151_Patient_1

tag: sample number


title: UAS_NonA_ADAR_REP2.fastq.gz

value: control


title: CHOP_134_Patient_1

tag: age


title: M1 CM treated A549

description: 2 days treatment

source_name: M1 macrophage conditioned media

tag: cell type


title: UAS_NonA_ADAR_REP1.fastq.gz


title: UCLA_150_Patient_1

tag: onset


title: CHOP_159_Patient_1


title: CHOP_118_Patient_1


title: UCLA_152_Patient_1


title: saline mPFC biological rep 6

city: Palo Alto

first: John

last: Huguenard

address: 1050A Arastradero Rd., Room A250

institute: Stanford University

hyb_protocol: Fragmented and labeled cDNA was hybridized to the Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide ((Thermo Fisher Scientific).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G and .CEL files were generated by Affymetrix GeneChip Command Console Software (Thermo Fisher Scientific).

data_processing: Microarrays were analyzed using Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific) with the SST-RMA algorithm. Default parameters were applied for assessment of differential expression. TAC 4.0 implements a linear mixed model analysis (LIMMA) package to identify differentially expressed genes. The significant genes were ranked by fold-change with a cutoff of 2 and ANOVA p-value less than 0.05.

source_name: mPFC of saline offspring at 4 mo.

label_protocol: Microarray was performed at the Protein and Nuclei Acid (PAN) Facility at Stanford University. The RNA integrity was examined on a Agilent 2100 bioanalyzer (Agilent Technologies). Only high quality RNA samples (RNA integrity number > 9) were used to generate double strand cDNA, which was fragmented and biotin labeled according to the Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher Scientific).

growth_protocol: To obtain control and MIA offspring, C57BL6/J mice (7-8 weeks old, Jackson Laboratory, stock no. 000664) were mated overnight and seminal plugs were examined daily, indicated as embryonic day (E0.5). Females with detectable plugs were weighed and individually housed.

extract_protocol: At 4 months of age, brains were harvested from poly(I:C) and saline offspring and the mPFC region was dissected out. Dissected cortices were homogenized and total RNA was isolated according to the manufacturer’s instructions using the RNAeasy Mini Kit (Qiagen, Stanford Translational Applications Service Center (TASC)).

treatment_protocol: On E12.5, pregnant (as ascertained by weight gain) females were injected intraperitoneally with a single dose of poly(I:C) (20 mg/kg, Invivogen) or saline. Each dam was subsequently returned its cage and left undisturbed until the birth of its litter. Pups were weaned between postnatal day 21-23 (P21-P23). Offspring were group-housed at maximum of 5 per cage with same-sex littermates.

tag: strain

tag: maternal treatment

value: saline

tag: tissue

value: brain (mPFC region)

value: male


title: saline mPFC biological rep 3

value: female


title: poly(I:C) mPFC biological rep 2

source_name: mPFC of poly(I:C) offspring at 4 mo.


title: saline mPFC biological rep 7


title: saline mPFC biological rep 2


title: CHOP_130_Patient_1

tag: duration


title: saline mPFC biological rep 8


title: neonatal non-gc3

city: White Oak

first: Mustafa

last: Akkoyunlu

address: 10903 New Hampshire Ave,

institute: FDA

hyb_protocol: Hybridization mixture of buffer, CodeSet, RNA sample was prepared for 16 hour incubation at 65 degrees. Strip tubes were placed into the automated nCounter Prep Station with reagents and consumables from the nCounter Master Kit

scan_protocol: Cartrige were placed into the nCounter Digital Analyzer for direct digital counting.

data_processing: Data in .RCC file were processed using nSolver software.

label: digital molecular barcode

source_name: Immunized neonatal spleen B cell

label_protocol: 100ng of total RNA in 5 ul of molecular grade water were subjected to hybridization step.

extract_protocol: >300,000 cells of adult mice and >15,000 cells from neonate mice per sample were lysed for RNA extraction using Quiagen microRNA isolation kit

tag: gender

value: pooled male and female

tag: developmental stage

value: neonatal

tag: treatment

value: immunization with sheep red blood cells

value: non-gc


title: saline mPFC biological rep 1


title: poly(I:C) mPFC biological rep 5


title: CHOP_136_Patient_1

city: Los Angeles

first: Daniel

last: Nachun

address: 695 Charles E Young Dr S

institute: UCLA

tag: batch

tag: site


title: saline mPFC biological rep 5


title: elev_REP2.fastq.gz

tag: tribe expression

value: induced

tag: rna

tag: sample type


title: saline mPFC biological rep 4

tag: Sex


title: UCLA_153_Patient_1

tag: pidn

tag: sample number

tag: rin

tag: status

tag: functional stage


title: neonatal non-gc2

tag: age

tag: strain

tag: cell type


title: elev_REP1.fastq.gz

value: nascent RNA


title: poly(I:C) mPFC biological rep 4

tag: maternal treatment

tag: tissue


title: poly(I:C) mPFC biological rep 3


title: CHOP_114_Patient_1

tag: onset

tag: duration


title: neonatal non-gc1

tag: gender

tag: developmental stage

tag: treatment


title: poly(I:C) mPFC biological rep 1


title: CHOP_115_Patient_1

tag: batch

tag: site


title: adult non-gc4

source_name: Immunized adult spleen B cell

value: adult


title: adult non-gc2


title: adult non-gc1


title: adult non-gc3


title: CHOP_108_Patient_1

tag: pidn

value: CHOP

tag: Sex


title: CHOP_113_Patient_2

tag: sample number

tag: rin

value: Patient


title: neonatal gc2

value: gc


title: CHOP_105_Patient_1

tag: status

value: FEMALE


title: neonatal gc1

tag: age


title: adult gc4

tag: strain


title: 44-Meso 96 MV

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.  After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment. RMA normalization is performed using R with Version 21 of Entrezgene CDF brain array.

label: Biotin

source_name: Meso 96 MV

label_protocol: 300 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

growth_protocol: 12 MPM cell lines that were established from patient pleural effusions, were maintained in RPMI-1640 medium supplemented with 10% heat-inactivated fetal calf serum, 100U/mL penicillin, 100μg/mL streptomycin and 2mM L-glutamine. 4 healthy cells cells were cultured in their specific media according to the manufacturers' recommendations.

extract_protocol: RNA was extracted using Nucleospin® RNA II kit (Macherey-Nagel)

treatment_protocol: 4 healthy cells and 12 malignant pleural mesothelioma cell lines were infected with measles virus (MV, MOI 1) or not infected (NI = basal expression) or were treated with type I interferon (IFN : IFN-alpha2 + IFN-Beta, 1000 UI/mL) during 48 hours.

tag: cell type

value: MPM cell line

tag: diagnosis

value: malignant pleural mesothelioma


title: CHOP_107_Patient_1


title: adult gc3


title: 42-Meso 76 IFN

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

source_name: Meso 76 IFN


title: 47-Meso 163 MV

source_name: Meso 163 MV


title: neonatal gc3


title: CHOP_90_Patient_1

tag: functional stage


title: CHOP_86_Patient_1

tag: onset


title: 43-Meso 96 NI

source_name: Meso 96 NI


title: adult gc2


title: CHOP_78_Patient_1

tag: duration


title: 46-Meso 163 NI

source_name: Meso 163 NI


title: CHOP_88_Patient_1


title: 41-Meso 76 MV

source_name: Meso 76 MV


title: CHOP_85_Patient_3

value: MALE


title: 45-Meso 96 IFN

source_name: Meso 96 IFN


title: CHOP_104_Patient_1

source_name: Whole blood


title: adult gc1

tag: gender


title: 48-Meso 163 IFN

source_name: Meso 163 IFN


title: neonatal non-tfh2

source_name: Immunized neonatal spleen T cell

tag: developmental stage

value: non-tfh


title: neonatal non-tfh1

tag: treatment


title: 38-Meso 47 MV

source_name: Meso 47 MV


title: adult non-tfh4

source_name: Immunized adult spleen T cell


title: 40-Meso 76 NI

source_name: Meso 76 NI


title: CHOP_69_Patient_1

tag: batch


title: adult non-tfh3


title: CHOP_71_Patient_1

tag: site


title: 36-meso 225 IFN

source_name: meso 225 IFN


title: 39-Meso 47 IFN

source_name: Meso 47 IFN


title: 37-Meso 47 NI

source_name: Meso 47 NI


title: adult non-tfh2


title: CHOP_67_Patient_1

tag: pidn


title: CHOP_68_Patient_1

tag: Sex


title: CHOP_66_Patient_2

tag: sample number


title: 34-meso 225 NI

source_name: meso 225 NI


title: neonatal tfh2

value: tfh


title: adult non-tfh1

value: female


title: neonatal tfh1

value: pooled male and female


title: 33-meso 31 IFN

source_name: meso 31 IFN


title: adult tfh4


title: 32-meso 31 MV

source_name: meso 31 MV


title: 35-meso 225 MV

source_name: meso 225 MV


title: 30-meso 13 IFN

source_name: meso 13 IFN


title: UCLA_56_Patient_1

value: UCLA

tag: rin


title: adult tfh3

value: immunization with sheep red blood cells


title: adult tfh2


title: adult tfh1


title: UCLA_58_Patient_1

tag: status


title: UCLA_57_Patient_1

tag: age


title: 29-meso 13 MV

source_name: meso 13 MV


title: PAD Patient 5 (81)

city: Leiden

first: Anne Yäel

last: Nossent

address: Albinusdreef 2

department: Department of Vascular Surgery

country: Netherlands

institute: Leiden University Medical Center

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
ABS1000081

hyb_protocol: None, no post-processing was preformed after isolation, RT and qPCR.

scan_protocol: No scanning or image processing was preformed.

data_processing:
Amplification curves were analysed using the Roche LC software, both for determination of Cq and for melt curve analysis. Amplification efficiency was calculated using Exiqon’s in-house algorithms similar to the LinReg software. Melting curves and temperatures of all assays were within specifications of the assays. All measurements with five Cqs less than the negative control and with a Cq < 37 were included in the analysis. Data that did not meet these criteria were omitted from further analyses. All data were normalized to the average of all assays in all samples (average Cq – assay Cq).
The amplification efficiency was calculated using algorithms similar to the LinReg software. All assays were inspected for distinct melting curves and the Tm was checked to be within known specifications for the assay. Furthermore assays must be detected with 5 Cqs less than the negative control, and with Cq<37 to be included in the data analysis. Data that did not pass these criteria were omitted from any further analysis. Cq was calculated as the 2nd derivative. Using NormFinder (Andersen CL, 2004) the best normalizer was found to be the average of assays detected in all samples.
All data was normalized to the average of assays detected in all samples (average – assay Cq).

source_name: Human Serum, pre-op

label_protocol: 7 ul RNA was reverse transcribed in 35 ul reactions using the miRCURY LNATM Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon). cDNA was diluted 50 x and assayed in 10 ul PCR reactions according to the protocol for miRCURY LNATM Universal RT microRNA PCR; each microRNA was assayed once by qPCR on the microRNA Ready-to-Use PCR, Serum/Serum Focus panel using ExiLENT SYBR Green master mix. Negative controls excluding template from the reverse transcription reaction was performed and profiled like the samples. The amplification was performed in a LightCycler 480 Real-Time PCR System (Roche) in 384 well plates. The amplification curves were analyzed using the Roche LC software, both for determination of Cq (by the 2nd derivative method) and for melting curve analysis.

extract_protocol: Total RNA was extracted from serum using the miRCURYTM RNA isolation kit – biofluids (Exiqon, Vedbaek, Denmark). Serum/Serum was thawed on ice and centrifuged at 3000 x g for 5 min in a 4°C microcentrifuge. An aliquot of 200 uL of serum/Serum per sample was transferred to a new microcentrifuge tube and 60 ul of Lysis solution BF containing 1ug carrier-RNA per 60ul Lysis Solution BF and RNA spike-in template mixture was added to the sample. The tube was vortexed and incubated for 3 min at room temperature, followed by addition of 20 uL Protein Precipitation solution BF. The tube was vortexed, incubated for 1 min at room temperature and centrifuged at 11,000 x g for 3 min. The clear supernatant was transferred to a new collection tube, and 270 uL isopropanol was added. The solutions were vortexed and transfer to a binding column. The column was incubated for 2 min at room temperature, and emptied using a vacuum-manifold. 100 uL wash solution 1 BF was added to the columns. The liquid was removed using a vacuum-manifold, and 700 uL wash solution 2 BF was added. The liquid was removed using a vacuum-manifold. 250ul wash solution was added and the column was spun at 11.000 x g to dry the columns entirely. The dry columns were transferred to a new collection tube and 50 uL RNase free H2O was added directly on the membrane of the spin column. The column was incubated for 1 min at room temperature prior to centrifugation at 11,000 x g. The RNA was stored in a -80°C freezer.

treatment_protocol: Samples were stored on ice until centrifugation (ten minutes, 2500g) at 4°C, after which serum was aliquoted and stored at -80°C until subsequent analysis.

tag: ethnicity

value: Dutch

value: male

tag: pad

value: End-stage Peripheral Artery Disease Patient

tag: time point

value: pre-op


title: Athlete 5 - After excerise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
2.5

source_name: Human Serum, t=0m

value: Norwegian

value: Elite Cyclist


title: Athlete 5 - 2 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
3.5

source_name: Human Serum, t=120m


title: CHOP_65_Patient_1

source_name: Whole blood

value: CHOP

value: Patient

tag: functional stage


title: 31-meso 31 NI

source_name: meso 31 NI

tag: cell type

value: MPM cell line

tag: diagnosis


title: Athlete 5 - Before exercise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
1.5

source_name: Human Serum, basline

value: basline


title: UCLA_62_Patient_1

value: FEMALE

tag: onset

tag: duration


title: 26-meso 11 MV

source_name: meso 11 MV

value: malignant pleural mesothelioma


title: UCLA_55_Patient_1

value: MALE


title: UCLA_46_Patient_1


title: 25-meso 11 NI

source_name: meso 11 NI


title: PAD Patient 4 (62)

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
ABS1000062


title: 24-meso 173 IFN

source_name: meso 173 IFN


title: Athlete 4 - 5 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
4.4

source_name: Human Serum, t=300m


title: 27-meso 11 IFN

source_name: meso 11 IFN


title: 28-meso 13 NI

source_name: meso 13 NI


title: 23-meso 173 MV

source_name: meso 173 MV


title: UCLA_42_Patient_1


title: UCLA_41_Patient_1


title: UCLA_40_Patient_1


title: Athlete 4 - 2 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
3.4


title: UCLA_44_Patient_1


title: 22-meso 173 NI

source_name: meso 173 NI


title: Athlete 4 - After excerise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
2.4


title: CHOP_37_Patient_1


title: 21-meso 61 IFN

source_name: meso 61 IFN


title: Athlete 4 - Before exercise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
1.4


title: CHOP_35_Patient_1


title: 20-meso 61 MV

source_name: meso 61 MV


title: UCLA_34_Patient_1


title: PAD Patient 3 (43)

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
ABS1000043


title: Athlete 3 - 5 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
4.3


title: Athlete 3 - 2 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
3.3


title: UCLA_31_Patient_1


title: 17-meso 45 MV

source_name: meso 45 MV


title: UCLA_38_Patient_1


title: Athlete 3 - Before exercise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
1.3


title: Athlete 3 - After excerise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
2.3


title: 18-meso 45 IFN

source_name: meso 45 IFN


title: 16-meso 45 NI

source_name: meso 45 NI


title: 19-meso 61 NI

source_name: meso 61 NI


title: PAD Patient 2 (25)

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
ABS1000025

source_name: Human Serum, pre-op


title: UCLA_27_Patient_1

source_name: Whole blood


title: UCLA_49_Patient_1


title: 14-meso 4 MV

source_name: meso 4 MV


title: CHOP_22_Patient_1


title: CHOP_26_Patient_1


title: CHOP_21_Patient_1


title: 13-meso 4 NI

source_name: meso 4 NI


title: Athlete 2 - 2 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
3.2

source_name: Human Serum, t=120m


title: 11-MESF MV

source_name: MESF MV

value: peritoneal mesothelial cells

value: healthy


title: UCLA_16_Patient_1

value: UCLA


title: 12-MESF IFN

source_name: MESF IFN


title: 10-MESF NI

source_name: MESF NI


title: Athlete 2 - After excerise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
2.2

source_name: Human Serum, t=0m


title: UCLA_15_Patient_1


title: Athlete 2 - Before exercise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
1.2

source_name: Human Serum, basline


title: UCLA_13_Patient_1


title: Athlete 2 - 5 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
4.2

source_name: Human Serum, t=300m


title: UCLA_11_Patient_1


title: PAD Patient 1 (10)

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
ABS1000010


title: CHOP_20_Patient_1


title: CHOP_7_Patient_1


title: CHOP_8_Patient_1


title: CHOP_6_Patient_1


title: 9-HMVEC IFN

source_name: HMVEC IFN

value: endothelial cells


title: 6-CCD19Lu IFN

source_name: CCD19Lu IFN

value: fibroblasts


title: CHOP_5_Patient_1


title: Athlete 1 - After excerise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
2.1

value: male


title: Athlete 1 - Before exercise

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
1.1


title: CHOP_9_Patient_1


title: 15-meso 4 IFN

source_name: meso 4 IFN


title: 2-CEB MV

source_name: CEB MV

value: lung epithelial cells


title: Athlete 1 - 2 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
3.1


title: 1-CEB NI

source_name: CEB NI


title: 3-CEB IFN

source_name: CEB IFN


title: 4-CCD19Lu NI

source_name: CCD19Lu NI


title: CHOP_1_Patient_1

source_name: Whole blood


title: 5-CCD19Lu MV

source_name: CCD19Lu MV


title: 12hpr_mock_input

status: Public on Jul 25 2018

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

data_processing:
The 3' end of the sequences were trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly G's using cutadapt.
Reads were aligned to the mouse mm10 genome using Bowtie2.
Aligned V3C-seq samples were sorted using Samtools, and the resulting aligned and sorted Bam files were converted to Bedgraph files using Bedtools.
ChIP-seq peaks were called using the SICER algorithm on EPIC software platform.
Quantile normalization of V3C-seq and ChIP-seq datasets were performed on Rstudio using the preprocessCore package.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: bed files from peak calling using EPIC
Supplementary_files_format_and_content: bedgraph calculated relative to raw reads
Supplementary_files_format_and_content: bedgraph, rpm calculated

source_name: Fibroblast

growth_protocol: Murine A9 fibroblasts were parasynchronized in Isoleucine-deficient DMEM media containing 5 percent FBS for 36-42 hours. Upon release into complete DMEM media, cells were infected with MVM at a Multiplicity of Infection of 5 for 12, 16, 20 or 20 hours (hpi: hours post infection), and samples were prepared for chromatin immunoprecipitation of chromosome conformation capture analyses.

extract_protocol:
For ChIP assays, lysates were clarified from sonicated nuclei (Diagenode), and DNA-protein complexes were immunoprecipitated using antibodies conjugated to Dynabeads (ThermoScientific). For Viral Chromosome Conformation Capture assays, MVM infected cells were crosslinked in 2 percent formaldehyde for 10 minutes, quenched in 0.125 M glycine for 5 minutes, collected and lysed in NP-40 containing 3C Lysis buffer for 10 minutes before being subjected to primary restriction enzyme digestion overnight with 400 U of HindIII. Following digestion, the restriction enzyme was inactivated and samples were subjected to intramolecular ligation with T4 DNA Ligase at room temperature. Samples were then reverse crosslinked and purified, before digesting in the secondary restriction enzyme, NlaIII. NlaIII was heat inactivated, samples were purified by phenol:chloroform purification, and circularized using T4 DNA Ligase. Samples were purified using a PCR Purification Kit (Qiagen), and equivalent amounts of DNA was used to perform inverse PCR with primers complementary to the MVMp genome. Inverse PCR samples were diluted 1:100 in TE, before being used as templates for nested-inverse PCR reactions. 6 independent neste-inverse  PCR reactions were pooled, PCR purified using a Qiagen kit and submitted for library preparation and high-throughput sequencing.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (cat # E7645L) according to manufacturer's instructions. Twelve samples were pooled per run and samples were analyzed by 75 bp single-end sequencing on the NextSeq 500 (Illumina).

treatment_protocol: Murine A9 fibroblasts were mock infected for 12 hours post release (hpr) from isoleucine deprivation, or treated with 2 mM Hydroxyurea for 12 hours (hpt: hours post treatment), before being harvested for chromatin immunoprecipitation.

tag: strain

tag: tissue

value: Subcutaneous connecive tissue

value: A9 fibroblast

tag: chip antibody


title: 16hpi_input


title: 20hpi_V3C_1

description: Inverse PCR product from 4C assay

data_processing:
Library strategy: V3C-seq
The 3' end of the sequences were trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly G's using cutadapt.
Reads were aligned to the mouse mm10 genome using Bowtie2.
Aligned V3C-seq samples were sorted using Samtools, and the resulting aligned and sorted Bam files were converted to Bedgraph files using Bedtools.
ChIP-seq peaks were called using the SICER algorithm on EPIC software platform.
Quantile normalization of V3C-seq and ChIP-seq datasets were performed on Rstudio using the preprocessCore package.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: bed files from peak calling using EPIC
Supplementary_files_format_and_content: bedgraph calculated relative to raw reads
Supplementary_files_format_and_content: bedgraph, rpm calculated


title: 24hpi_V3C_1

description: Inverse PCR product from 4C assay


title: 16hpi_V3C_1

description: Inverse PCR product from 4C assay


title: 20hpi_V3C_2

description: Inverse PCR product from 4C assay


title: 16hpi_V3C_2

description: Inverse PCR product from 4C assay


title: 24hpi_V3C_2

description: Inverse PCR product from 4C assay


title: CHOP_4_Patient_1

tag: pidn

tag: batch

tag: site


title: 16hpi_V3C_3

description: Inverse PCR product from 4C assay


title: 12hpi_V3C_1

description: Inverse PCR product from 4C assay


title: 16hpi_brca1_1

value: ThermoFisher #17F8 (5 ug)


title: 12hpi_V3C_2

description: Inverse PCR product from 4C assay


title: 16hpi_brca1_2


title: 16hpi_ns1_2

description: Mouse Anti-NS1 antibody was generated at the MU Hybridoma core (Salome and Pintel, unpublished) and was purified using HiTrap Protein G columns (GE Lifesciences). Anti-NS1 antibody was validated using western blots, immunofluorescense and immunoprecipitation.

value: Mouse anti-NS1 monoclonal (10 ug)


title: 12hpt_hu_gh2ax_2

value: Millipore #05-636 (5 ug)


title: 20hpi_gh2ax_2


title: 12hpt_hu_gh2ax_1


title: 20hpi_gh2ax_1


title: 16hpi_gh2ax_2


title: 16hpi_gh2ax_1


title: 12hpr_mock_gh2ax_1


title: 12hpr_mock_gh2ax_2


title: testisB_28

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

institute: UPenn Perelman SOM and CHOP

data_processing:
Reads were aligned to mm10 RefSeq using Bowtie software in a sequencial manner first to rRNA, snRNA and miRNAs to eliminate any reads coming from them and then aligned to the genome.
Genome_build: mm10
Supplementary_files_format_and_content: excel file with normalized gene counts (in multiple spreadsheets)

source_name: testisB

growth_protocol: After fertilization by ICSI Zygotes developed in KSOM medium at 37 °C in 5% CO2 5% O2 for 28 hours

extract_protocol:
Embryos were collected at 28 hours post-ICSI in 5ul of buffer TCL with 1% beta mercaptoethanol and frozen at -80C.
single-cell RNA-seq/Nextera kit
single embryo RNA-seq (Smart-seq 2 protocol)

treatment_protocol: Zygotes were generated by ICSI from sperm isolated from the testis, caput epididymis, or cauda epididiymis. Following fertilization by ICSI zygotes were developed to different stages of preimplantation development and were harvested for single-embryo RNA-Seq (Smart-Seq 2 protocol). For RNA injection experiments 3 hours after fertilization by ICSI RNA was injected using an Eppendorf Femtojet injection setup.

value: FVB

tag: deveopmental stage

value: Blastocyst

tag: sperm source

value: testis

tag: rna injected


title: testisB_9


title: testisB_6


title: testisB_27


title: testisB_3


title: testisB_8


title: testisB_26


title: testisB_25


title: testisB_5


title: testisB_4


title: testisB_24


title: 16hpi_ns1_1


title: testisB_23


title: testisB_22


title: testisB_2


title: testisB_21


title: testisB_20


title: testisB_19


title: testisB_18


title: testisB_15


title: testisB_16


title: testisB_17


title: testisB_14


title: testisB_13


title: testisB_12


title: testisB_7


title: testisB_10


title: testisB_11


title: testisB_1


title: cauB_9

source_name: cauB

value: cauda


title: cauB_7


title: cauB_6


title: cauB_4


title: cauB_3


title: cauB_29


title: cauB_5


title: cauB_27


title: cauB_28


title: cauB_22


title: cauB_24


title: cauB_23


title: cauB_26


title: cauB_25


title: cauB_21


title: cauB_20


title: cauB_2


title: cauB_17


title: cauB_19


title: cauB_16


title: cauB_8


title: cauB_15


title: cauB_14


title: cauB_12


title: cauB_11


title: cauB_10


title: cauB_13


title: testisM_7

source_name: testisM

value: Morula


title: testisM_9


title: cauB_1


title: 8-HMVEC MV

source_name: HMVEC MV


title: testisM_6


title: testisM_4


title: testisM_5


title: testisM_33


title: testisM_32


title: testisM_34


title: testisM_3


title: testisM_29


title: testisM_30


title: cauB_18


title: testisM_27


title: testisM_26


title: testisM_28


title: testisM_24


title: testisM_23


title: testisM_8


title: testisM_22


title: testisM_20


title: testisM_2


title: testisM_19


title: testisM_18


title: testisM_15


title: testisM_16


title: testisM_31


title: testisM_14


title: testisM_13


title: testisM_12


title: testisM_11


title: testisM_10


title: testisM_1


title: cauM_9

source_name: cauM


title: cauM_8


title: cauM_7


title: testisM_25


title: cauM_6


title: cauM_5


title: cauM_4


title: cauM_34


title: cauM_33


title: cauM_32


title: testisM_21


title: testisM_17


title: cauM_3


title: cauM_31


title: cauM_29


title: cauM_27


title: cauM_25


title: cauM_26


title: cauM_28


title: cauM_22


title: cauM_24


title: cauM_21


title: cauM_23


title: cauM_2


title: cauM_18


title: cauM_17


title: cauM_15


title: cauM_16


title: cauM_14


title: cauM_13


title: cauM_12


title: cauM_10


title: cauM_30


title: cauM_1


title: testis4C_9

value: 4C embryo


title: testis4C_8


title: testis4C_7


title: testis4C_6


title: testis4C_4


title: testis4C_5


title: testis4C_34


title: cauM_20


title: testis4C_30


title: testis4C_31


title: testis4C_33


title: testis4C_32


title: testis4C_29


title: 7-HMVEC NI

source_name: HMVEC NI

value: healthy


title: cauM_19


title: testis4C_28


title: Athlete 1 - 5 hours of rest

description:
Exiqon/Qiagen Focus Panel of in-house known circulating microRNAs, consisting of in total 179 different microRNAs. All in all, 130 different microRNAs were detected.
4.1

source_name: Human Serum, t=300m

tag: ethnicity

value: Norwegian

tag: Sex

value: Elite Cyclist


title: testis4C_3


title: testis4C_25


title: testis4C_26


title: testis4C_27


title: testis4C_24


title: testis4C_23


title: cauM_11


title: testis4C_21


title: testis4C_2


title: testis4C_20


title: testis4C_18


title: testis4C_19


title: testis4C_17


title: testis4C_16


title: testis4C_15


title: testis4C_14


title: testis4C_13


title: testis4C_11


title: testis4C_12


title: cau4C_9


title: cau4C_8


title: testis4C_10


title: CHOP_2_Patient_1

tag: sample number

value: CHOP

tag: rin

tag: status

value: Patient

value: FEMALE

tag: age


title: cau4C_6


title: cau4C_7


title: cau4C_4


title: cau4C_32


title: cau4C_5


title: cau4C_33


title: testis4C_22


title: cau4C_29


title: cau4C_30


title: cau4C_3


title: testis4C_1


title: cau4C_31


title: cau4C_27


title: cau4C_26


title: cau4C_25


title: cau4C_22


title: cau4C_21


title: cau4C_24


title: cau4C_20


title: cau4C_23


title: cau4C_18


title: cau4C_19


title: cau4C_2


title: cau4C_17


title: cau4C_16


title: cau4C_15


title: cau4C_14


title: cau4C_13


title: cau4C_12


title: cau4C_11


title: cau4C_10


title: tRF_B_9

source_name: tRF

value: caput

value: EpiM tRF


title: cau4C_1


title: tRF_B_8


title: tRF_B_5


title: tRF_B_6


title: tRF_B_7


title: tRF_B_4


title: tRF_B_30


title: tRF_B_29


title: tRF_B_28


title: tRF_B_27


title: tRF_B_31


title: tRF_B_3


title: tRF_B_26


title: tRF_B_25


title: tRF_B_23


title: tRF_B_24


title: tRF_B_21


title: tRF_B_2


title: tRF_B_22


title: tRF_B_18


title: tRF_B_20


title: tRF_B_17


title: tRF_B_16


title: tRF_B_15


title: tRF_B_12


title: tRF_B_13


title: tRF_B_14


title: tRF_B_11


title: tRF_B_1


title: miRNA_B_7

source_name: miRNA

value: EpiM miRNA


title: miRNA_B_9


title: miRNA_B_5


title: miRNA_B_4


title: miRNA_B_6


title: miRNA_B_29


title: miRNA_B_30


title: miRNA_B_32


title: miRNA_B_28


title: miRNA_B_3


title: miRNA_B_27


title: miRNA_B_26


title: miRNA_B_24


title: miRNA_B_23


title: miRNA_B_22


title: miRNA_B_2


title: miRNA_B_19


title: miRNA_B_18


title: miRNA_B_17


title: miRNA_B_20


title: miRNA_B_15


title: tRF_B_10


title: miRNA_B_13


title: miRNA_B_12


title: miRNA_B_8


title: miRNA_B_10


title: caputB_8

source_name: caputB


title: caputB_7


title: miRNA_B_1


title: caputB_4


title: caputB_33


title: miRNA_B_25


title: caputB_31


title: caputB_32


title: caputB_30


title: caputB_3


title: caputB_28


title: caputB_27


title: miRNA_B_16


title: caputB_23


title: miRNA_B_14


title: caputB_22


title: caputB_21


title: caputB_20


title: miRNA_B_11


title: caputB_2


title: caputB_18


title: caputB_17


title: caputB_6


title: caputB_9


title: caputB_5


title: caputB_14


title: caputB_16


title: caputB_15


title: caputB_12


title: caputB_13


title: caputB_10


title: caudB_8

source_name: caudB


title: caputB_11


title: caputB_1


title: caputB_29


title: caputB_24


title: caudB_6


title: caudB_7


title: caudB_9


title: caudB_5


title: caputB_26


title: caputB_19


title: caudB_31


title: caudB_30


title: caudB_29


title: caudB_3


title: caudB_28


title: caudB_27


title: caudB_26


title: caudB_25


title: caudB_23


title: caudB_24


title: caudB_22


title: caudB_21


title: caudB_2


title: caudB_15


title: caudB_18


title: caudB_19


title: caudB_16


title: caudB_13


title: caudB_4


title: caudB_14


title: caudB_11


title: caudB_10


title: caudB_1


title: caudB_12


title: trf4C_7


title: trf4C_5


title: trf4C_3


title: trf4C_9


title: trf4C_8


title: trf4C_22


title: trf4C_24


title: trf4C_21


title: trf4C_2


title: trf4C_20


title: trf4C_4


title: caudB_20


title: trf4C_16


title: trf4C_17


title: trf4C_23


title: caudB_17


title: trf4C_15


title: trf4C_14


title: cau4C_28


title: trf4C_11


title: trf4C_1


title: mi4C_9


title: trf4C_12


title: trf4C_13


title: mi4C_5


title: mi4C_8


title: mi4C_3


title: mi4C_4


title: mi4C_24


title: mi4C_7


title: mi4C_23


title: mi4C_21


title: mi4C_22


title: mi4C_16


title: mi4C_15


title: mi4C_13


title: mi4C_19


title: mi4C_20


title: mi4C_2


title: mi4C_18


title: mi4C_17


title: mi4C_12


title: mi4C_11


title: mi4C_10


title: mi4C_1


title: cp4C_9


title: trf4C_10


title: cp4C_7


title: cp4C_5


title: cp4C_3


title: cp4C_8


title: cp4C_6


title: cp4C_24


title: cp4C_4


title: cp4C_21


title: cp4C_22


title: cp4C_19


title: cp4C_20


title: cp4C_17


title: cp4C_18


title: cp4C_2


title: cp4C_16


title: cp4C_12


title: cp4C_11


title: ca4C_9


title: cp4C_14


title: ca4C_6


title: ca4C_7


title: ca4C_5


title: cp4C_10


title: cp4C_13


title: ca4C_4


title: ca4C_3


title: ca4C_8


title: ca4C_24


title: cp4C_23


title: ca4C_23


title: ca4C_22


title: ca4C_21


title: ca4C_20


title: ca4C_19


title: ca4C_18


title: cp4C_1


title: ca4C_12


title: ca4C_13


title: ca4C_16


title: ca4C_15


title: ca4C_17


title: ca4C_11


title: ca4C_10


title: Caput_epi_0204_1

source_name: Caput

value: EpiM small RNA


title: ca4C_2


title: ca4C_14


title: Caput_epi1_0212_3


title: Caput_epi1_0207_1


title: Caput_epi1_0213_1


title: Caput_epi_0205_3


title: Caput_epi1_0208_1


title: Caput_epi2_0207_1


title: Caput_epi1_0208_4


title: Caput_epi_0204_4


title: Caput_epi1_0208_6


title: Caput_epi2_0207_3


title: Caput_epi2_0207_2


title: Caput_epi1_0208_3


title: Caput_epi1_0212_1


title: Caput_epi_0204_3


title: Caput_epi1_0208_5


title: Caput_epi_0205_2


title: Caput_epi_0204_2


title: Caput_epi2_0207_6


title: Caput_epi2_0207_5


title: Caput_epi2_0208_1


title: Caput_epi2_0207_4


title: Caput_epi1_0208_2


title: Caput_gfp1_0208_1

value: GFP


title: Caput_gfp1_0208_2

value: FVB


title: Caput_gfp_0205_1

value: Blastocyst


title: Caput_gfp_0204_1


title: Caput_gfp1_0208_3


title: Caput_gfp1_0212_1


title: Caput_epi2_0213_1


title: Caput_gfp1_0211_2


title: Caput_gfp1_0211_1


title: Caput_gfp1_0211_4


title: Caput_epi2_0213_2


title: Caput_gfp1_0211_3


title: Caput_gfp1_0212_2


title: Caput_gfp2_0207_2


title: Caput_gfp2_0207_3


title: Caput_gfp2_0207_5


title: Caput_gfp2_0208_6


title: Caput_gfp2_0208_5


title: Caput_gfp2_0212_2


title: Caput_gfp2_0208_3


title: Caput_gfp2_0207_6


title: Caput_gfp2_0208_2


title: Caput_gfp2_0207_1


title: Cauda_0204_2

source_name: Cauda


title: Cauda_0204_4


title: Caput_gfp2_0207_7


title: Cauda_0205_1


title: Caput_gfp2_0208_4


title: Cauda_0204_3


title: Cauda_0205_2


title: Cauda_0204_1


title: Cauda_0204_5


title: Caput_gfp1_0212_4


title: Caput_gfp1_0212_3


title: Caput_gfp2_0207_4


title: Cauda_0205_4


title: Cauda_0205_3


title: Cauda_1_0207_1


title: Cauda_1_0207_2


title: Cauda_1_0208_2


title: Cauda_1_0208_4


title: Cauda_1_0208_1


title: Cauda_1_0208_3


title: Cauda_1_0211_1


title: Cauda_1_0207_3


title: Cauda_1_0207_4


title: Cauda_1_0212_1


title: Cauda_1_0212_2


title: Cauda_2_0207_2


title: Cauda_1_0211_5


title: Cauda_1_0211_2


title: Cauda_2_0211_2


title: Cauda_2_0211_1


title: Cauda_2_0211_3


title: Cauda_2_0208_4


title: Cauda_2_0207_3


title: Cauda_2_0207_4


title: Cauda_2_0211_4


title: Cauda_1_0211_3


title: Cauda_2_0212_1


title: Cauda_1_0211_4


title: Cauda_2_0212_2


title: Cauda_2_0208_1


title: Cauda_2_0208_3


title: Cauda_2_0212_3


title: Cauda_2_0212_4


title: CaputBlast9


title: CaputBlast8


title: Cauda_2_0207_1


title: CaputBlast7


title: CaputBlast6


title: CaputBlast4


title: CaputBlast5


title: CaputBlast34


title: CaputBlast35


title: CaputBlast33


title: CaputBlast30


title: CaputBlast3


title: CaputBlast25


title: CaputBlast26


title: CaputBlast29


title: CaputBlast28


title: CaputBlast31


title: CaputBlast22


title: CaputBlast18


title: CaputBlast19


title: CaputBlast2


title: CaputBlast16


title: CaputBlast15


title: CaputBlast20


title: CaputBlast21


title: CaputBlast32


title: CaputBlast14


title: CaputBlast17


title: CaputBlast12


title: CaputBlast11


title: CaputBlast23


title: CaputBlast24


title: CaputBlast10


title: CaputBlast1


title: CaudaBlast9


title: CaudaBlast8


title: CaudaBlast7


title: CaudaBlast6


title: CaudaBlast5


title: CaudaBlast40


title: CaudaBlast39


title: CaudaBlast37


title: CaudaBlast38


title: CaudaBlast4


title: CaudaBlast36


title: CaputBlast13


title: CaudaBlast35


title: CaudaBlast34


title: CaudaBlast33


title: CaudaBlast32


title: CaudaBlast30


title: CaudaBlast27


title: CaudaBlast29


title: CaudaBlast28


title: CaudaBlast3


title: CaudaBlast31


title: CaudaBlast24


title: CaudaBlast11


title: CaudaBlast18


title: CaudaBlast20


title: CaudaBlast25


title: CaudaBlast10


title: CaudaBlast1


title: CaudaBlast12


title: CaudaBlast26


title: CaudaBlast13


title: CaudaBlast23


title: CaudaBlast14


title: CP_B_8

source_name: CP


title: CP_B_7


title: CP_B_9


title: CP_B_4


title: CaudaBlast15


title: CaudaBlast19


title: CaudaBlast22


title: CaudaBlast17


title: CaudaBlast21


title: CaudaBlast2


title: CP_B_36


title: CP_B_34


title: CP_B_33


title: CP_B_32


title: CP_B_37


title: CP_B_6


title: CP_B_31


title: CP_B_28


title: CP_B_21


title: CP_B_22


title: CP_B_26


title: CP_B_20


title: CP_B_16


title: CP_B_14


title: CP_B_15


title: CP_B_30


title: CP_B_27


title: CP_B_2


title: CP_B_11


title: CP_B_10


title: CP_B_17


title: CP_B_38


title: CP_B_13


title: CP_B_35


title: CA_B_7

source_name: CA


title: CA_B_6


title: CA_B_8


title: CP_B_1


title: CA_B_5


title: CP_B_23


title: CA_B_9


title: CP_B_12


title: CP_B_29


title: CP_B_18


title: CP_B_25


title: CA_B_44


title: CP_B_24


title: CA_B_38


title: CA_B_4


title: CA_B_41


title: CA_B_37


title: CA_B_39


title: CA_B_40


title: CA_B_36


title: CA_B_42


title: CA_B_33


title: CA_B_32


title: CA_B_3


title: CA_B_29


title: CA_B_30


title: CA_B_34


title: CA_B_28


title: CA_B_25


title: CA_B_27


title: CA_B_24


title: CA_B_26


title: CA_B_22


title: CA_B_20


title: CA_B_19


title: CA_B_23


title: CA_B_21


title: CA_B_43


title: CA_B_17


title: CA_B_18


title: CA_B_16


title: CA_B_14


title: CA_B_35


title: CA_B_15


title: CA_B_1


title: CaudaM_7

source_name: CaudaM


title: CA_B_13


title: CaudaM_9


title: CA_B_31


title: CaudaM_6


title: CA_B_11


title: CaudaM_32


title: CaudaM_31


title: CaudaM_5


title: CaudaM_30


title: CaudaM_3


title: CaudaM_28


title: CaudaM_29


title: CaudaM_27


title: CaudaM_26


title: CaudaM_25


title: CaudaM_23


title: CaudaM_24


title: CaudaM_21


title: CaudaM_22


title: CaudaM_20


title: CA_B_12


title: CaudaM_19


title: CaudaM_2


title: CaudaM_18


title: CaudaM_17


title: CaudaM_11


title: CaudaM_14


title: CaudaM_16


title: CaudaM_12


title: CaudaM_1


title: CaudaM_13


title: CaudaM_10


title: CaudaM_4


title: CaputM_8

source_name: CaputM


title: CaputM_9


title: CaputM_5


title: CaputM_7


title: CaputM_32


title: CaputM_6


title: CaputM_30


title: CaputM_4


title: CaputM_31


title: CaputM_29


title: CaputM_28


title: CaputM_27


title: CaputM_3


title: CaputM_26


title: CaputM_25


title: CaputM_24


title: CaputM_23


title: CaputM_22


title: CaputM_20


title: CaudaM_15


title: CaputM_15


title: CaputM_13


title: CaputM_18


title: CaputM_19


title: CaputM_11


title: CaputM_10


title: CaputM_12


title: CaputM_1


title: CP_8C_9

value: 8C embryo


title: CP_8C_33


title: CP_8C_4


title: CP_8C_35


title: CP_8C_32


title: CP_8C_31


title: CP_8C_34


title: CP_8C_30


title: CP_8C_26


title: CP_8C_27


title: CP_8C_24


title: CP_8C_28


title: CP_8C_22


title: CP_8C_23


title: CP_8C_20


title: CP_8C_25


title: CaputM_16


title: CaputM_17


title: CP_8C_21


title: CP_8C_14


title: CP_8C_15


title: CP_8C_17


title: CP_8C_13


title: CP_8C_12


title: CP_8C_18


title: CP_8C_10


title: CA_8C_9

value: cauda


title: CA_8C_7


title: CA_8C_5


title: CP_8C_1


title: CP_8C_3


title: CA_8C_4


title: CA_8C_30


title: CA_8C_3


title: CA_8C_24


title: CA_8C_27


title: CA_8C_26


title: CA_8C_25


title: CA_8C_29


title: CA_8C_21


title: CA_8C_23


title: CA_8C_19


title: CP_8C_16


title: CA_8C_17


title: CA_8C_18


title: CP_8C_2


title: CA_8C_20


title: CA_8C_14


title: CA_8C_16


title: CA_8C_13


title: CA_8C_11


title: CA_8C_10


title: CA_8C_8


title: caput4C_9


title: caput4C_8


title: caput4C_4


title: caput4C_6


title: Caput4C_32


title: caput4C_5


title: Caput4C_31


title: caput4C_3


title: CA_8C_2