title: Pc RNA Helicos

source_name: S2 cell line

extract_protocol:
Soluble chromatin was incubated with IgG agarose beads (Sigma, Cat # A2909). For every 10 ml of sonicated chromatin, 0.5-1 ml beads were added (for 50 ml of 3rd instar larvae or adult fly chromatin 1 ml beads was used). The mixture was rotated end-over end in the 15 ml Falcon tubes for 12-16 h at +4°C. Beads were then washed 3 times for 10 min at +4°C with 15 bead volumes of RIPA buffer and spun down for 5 min at 1000g, +4°C between washes. Beads were then washed for 10 min with 15 bead volumes of buffer TEN 140 buffer with 0.1% Triton X-100 at +25°C and spun down for 5 min at 1000 g, +25°C. In order to elute the complexes (protein-DNA-RNA), 12-15 bead volumes of IgG Elution buffer were added to the beads. The slurry was mixed by inversion for 1 hour at +25°C. This elution step was repeated one more time. In order to eliminate urea from the samples, the eluates were first concentrated  in 10K Amicon Ultra-15 columns (3000g, 15min at +25°C) and then washed/buffer exchanged 3 times with 15 ml of TEN 140 buffer with 0.1% Triton X100 (3000g, 5-15min at +25°C) in a fresh Amicon column. The resulting 0.5 ml concentrate was diluted with 2500 ul of RIPA buffer and transferred into two Eppendorf tubes.  Biotin-Streptavidin affinity purification   150-300 ul of Streptavidin Agarose beads (Thermo Scientific, cat # 20349) were added to each tube.  The mixture was rotated end-over-end for 12-16 hours at +16°C. Beads from both tubes were pooled into one 15 ml Falcon tube washed once with RIPA buffer, once with TEN 140 buffer with 0.1% Triton X100, twice with IgG Elution buffer and twice with IgG Elution buffer without SDS. For each washing step, beads were mixed with 12 ml of a given buffer on a rotating wheel for 10 min at +25°C and spun down for 5 min at 1000 g, +25°C. Beads were re-suspended in 10 ml of TEN 140 buffer and divided into three tubes: 6 ml for protein work, 2 ml for DNA and 2 ml for RNA analysis.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments from 300-700 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's

value: embryo

value: Pc BioTAP

tag: platform

value: Helicos

value: RNA fraction of the BioTAP-XL pulldowns


title: HP1a RNA Helicos

status: Public on Jul 03 2014

type: SRA

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Illumina base-calling pipeline; Heclios base-calling pipeline
for Illumina data: aligned to dm3 using bowtie (-t 1 -k 1); Helicos data was aligned using helisphere pipeline with default parameters, and uniquely aligned reads only.
smoothed enrichment calculated using SPP (http://compbio.med.harvard.edu/Supplements/ChIP-seq/), get.smoothed.enrichment.mle().
Genome_build: dm3 for D.melanogaster
Supplementary_files_format_and_content: bedGraph files containing either smoothed enrichment MLE (*IP.bedGraph), or strand-specific smoothed read density (*pos.bedGraph; *neg.bedGraph)

molecule: total RNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Drosophila S2 cells were grown in four 50 ml large T-flasks (225 cm2) in 10% FBS –supplemented Schneider’s Drosophila medium (Invitrogen Cat # 11720) to a density of ~5x106 cells/ml. Cell cultures were split in half by adding an equal volume of HyClone CCM3 serum-free medium (Thermo Scientific, Cat No.SH30065) and grown in eight T-flasks (225 cm2) to a density of ~5x106 cells/ml. Cells were transferred into four 2.8L Fernbach glass flasks (Bellco, Glass Inc.). To generate 100 g of 6-20 hr embryos, flies were grown at 25°C with 65% humidity using large embryo collection cages (Flystuff cat. N. 59-101) containing molasses plates with yeast paste. 100 g of 3rd instar larvae or adult flies were used. Larvae were separated from the food by washing in 20% sucrose (see Ashburner, 1989). Flies were collected 1-12 hours after eclosion.

treatment_protocol: Harvested S2 cells were homogenized by using a 100 ml Dounce homogenizer (Bellco, Glass Inc.), 10 strokes of each of A and B pestles. For every 4-5 ml of cell pellet volume 100 ml of NEB buffer+0.1 mM PMSF pre-chilled on ice were added. Without delay, 100 ml of cell/nuclear homogenate was poured into a T-225 flask containing a room-temperature mixture of 360 ml of PBS and 40 ml of 37% formaldehyde and incubated for 30 min at 25°C on a orbital shaker platform with vigorous shaking (100rpm). Fixed nuclei were pelleted by spinning for 10 min at 4000 g, +4°C. The supernatant was carefully decanted and the nuclear pellet was washed four times with 100 ml of ice-cold PBS with 0.1 mM PMSF. Nuclei were pelleted between washes for 10 min at 4000g, +4°C. Nuclei were resuspended in glycerol buffer and snap-frozen in liquid N2 prior to further processing. Frozen nuclear extracts from Drosophila S2 cells, embryos, 3rd instar larvae or adult flies were thawed and spun down for 10 min at 4000 g, +4°C. Pellets were washed with 10-20 volumes of TE buffer with 0.1 mM PMSF and spun down for 10 min at 4000g, +4°C. Pellets were again re-suspended with 10 volumes of TE buffer with 0.1 mM PMSF by pipetting up and down (for 3rd instar larval or adult fly chromatin, a motorized Teflon pestle was used). SDS was added to the mixture to a final concentration of 1%. The mixture was inverted in the tube 10 times and spun down for10 min at 4000 g, +4°C. The supernatant was carefully removed (Note: the pellet may be quite loose) and the pellet was re-suspended with 10 volumes of TE buffer with 0.1 mM PMSF by pipetting and further spun down for 10 min at 4000 g, +4°C. This washing step was repeated twice. The pellet was re-suspended with 1.5 volumes of TE buffer with 0.1 mM PMSF by pipetting up and down (for 3rd instar larvae or adult flies motorized Teflon pestle had been used). SDS was added to a mixture to a final concentration of 0.1%. The resulting viscous mixture was sonicated in 4.5 ml aliquots using a Misonix Sonicator 3000 with Microtip power output level 7 and total sonication processing time of 3.5 min, 15 sec pulse “on” and 45 sec “off” time to generate DNA fragments in the range of 300-2000 bp.   Triton X-100 (1% final) and NaCl (140 mM final) were added to the sonicated samples. Samples were mixed on a rotating wheel for 5 min  at +4C and spun down for 10 min at 10000 g, +4°C. The supernatant containing the soluble chromatin was collected. Note: In order to control for chromatin input composition and quality (for protein, DNA and RNA), a 1 ml aliquot is reserved before proceeding with the next step.

tag: tissue

tag: pull-down tag

value: HP1a BioTAP

tag: molecule subtype


title: TC-1-001_milk

city: Meath

first: Nathan

last: Lawless

address: Grange

country: Ireland

institute: Teagasc

data_processing:
Illumina CASAVA 1.4
FASTQC v0.10.0
Fastq Illumina filter v0.1
Cutadapt v1.2
Fastq quality filter package v0.0.13.2
novoalign v2.08.03
HTSeq-count v 0.5.3p3
Genome_build: UMD3.1 assembly
Supplementary_files_format_and_content: All files processed as fastq files, converted to SAM format using samtools v 0.1.18

organism: Bos taurus

source_name: Monocyte

growth_protocol: Milk and blood derived CD14+ monocytes were isolated by FACS, cells were labelled with monoclonal anti-bovine CD14 IgG1 and a PE-conjugated anti-mouse IgG antibody. Labelled cells were separated based on fluorescence intensity using the BD FACS Aria Cell Sorting System. Cells with greater than 95% purity were isolated from milk from the infected/control gland and peripheral blood of each animal .

extract_protocol:
MicroRNA was extracted using mirPremierTM microRNA Isolation Kits (Sigma-Aldrich, Steinheim, Germany.) following the manufacturer's instructions
One-hundred indexed miRNA libraries were prepared for cluster generation using the TruSeq Small RNA sample preparation kit (50 cycles). Procedures were performed according to the manufacturer’s protocol.

treatment_protocol: An inoculation load of 500 CFU of S. uberis in 1 mL of saline was administered through the teat canal of the front right quarter. One control animal (inoculated with saline) was run alongside the infected animal under the same conditions as described above. Milk and blood samples were obtained from each animal at 0, 12, 24, 36 and 48 hrs post-infection (or mock infection).

tag: breed

value: Holstein Friesian

tag: cell type

value: CD14 + milk derived monocytes

tag: preperation kit

value: Indexed TruSeq small RNA sample preparation kit (50 cycles)

tag: infection

value: Control

tag: time

value: 0 h


title: MSL3 RNA Helicos

tag: cell line background

value: MSL3 BioTAP


title: F3

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Base calls and quality scores were generated using Illumina's Real-Time Analysis software v1.8.7.  Binary base call files were converted to text formatted qseq files via OLB 1.9.0, which were then filtered and converted to fastq format by CASAVA 1.7, using the default Chastity threshold of 0.6.
Read counts for the genes are collected by Bioconductor Biostrings and IRanges packages.  Reads that are mapped ambiguously to M locations are counted as 1/M at each occurrence.
Genome_build: hg19
Supplementary_files_format_and_content: biopsy.gene.counts.csv.gz contains the read counts for each gene for FSHD/control biopsy samples
Supplementary_files_format_and_content: cultured.gene.counts.csv.gz contains the read counts for each gene for myotubes and myoblasts from FSHD/control samples

organism: Homo sapiens

source_name: Female FSHD1 biopsy F3

growth_protocol: Muscle cell cultures: Muscle cells derived from two FSHD1 and three FSHD2 were cultured and RNA was harvested from both myoblasts and myotubes. These cultures were described previously (24). As previously described, Primary myoblast cell lines were received from the University of Rochester biorepository (http://www.urmc.rochester.edu/fields-center) and were cultured in DMEM/F-10 media (Gibco) in the presence of 20% heat-inactivated fetal bovine serum (Gibco), 1% penicillin/streptomycin (Gibco). Media was supplemented with 10ng/ml rhFGF (Promega) and 1μM dexamethasone (SIGMA). Myoblasts were fused at 80% confluence in DMEM/F-12 Glutamax media containing 2% KnockOut serum replacement formulation (Gibco) for 36 hours.

extract_protocol:
Muscle biopsy samples were obtained under local anesthesia by the minimally needle biopsy technique utilizing the modified Bergstrom needle. RNA was extracted, poly(A) selected, and subjected to Illumina sequencing using standard protocols to generate 100bp  single-end reads.
Sequencing libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

tag: gender

value: Female

value: FSHD1 Muscle biopsy


title: E3131

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description: ribosomal depleted RNA

data_processing:
Base calling and primary analysis was performed using Torrent Suite 4.0.2
Reads were quality trimmed (PHRED 20) with CLC Genomics Server 6.0
Mapped to Ensembl genes (Ovis aries Oar_v3.1.75) with CLC Genomics Server 6.0
Filtered reads at RPKM ≥ 5 in all samples
Genome_build: Ensembl Oar_v3.1.75
Supplementary_files_format_and_content: Processed file includes expression values (RPKM) for each sample with gene symbol and description from Ensembl 75. The RawData tab includes all genes and the RPKM5 tab includes only genes with RPKM ≥ 5 in all samples

organism: Ovis aries

source_name: conceptus

growth_protocol: In utero conceptus development

extract_protocol:
Frozen conceptus samples were homogenized in RLT plus buffer and RNA was isolated using RNeasy Plus kit (Qiagen). RNA samples were depleted of ribosomal RNA using Ribominus system (Ambion).
20ng of ribosomal depleted sample and the Ion Total RNA-seq Kit v2 (Life Technologies) were used to construct strand specific sequencing libraries, with several deviations from the protocol.  Enzymatic RNA fragmentation was carried out at 37 C for 90 seconds.  Fragmented RNA was purified using 1.0X AMPure XP beads (Beckmann-Coulter Genomics).  cDNA and the final libraries were purified with 0.8X AMPure XP beads.   Emulsion PCR was performed on an Ion One Touch 2 instrument, using the Ion P1 Template OT2 200 v3 reagents.  Sequencing beads were quantified and evaluated by flow cytometry (Millipore Guava Easy Cyte) with Sybr Gold (Molecular Bioprobes) before loading on an Ion P1 semiconductor sequencing chip.  Sequencing was performed on an Ion Proton using Ion P1 200 v3 sequencing reagents and 440 flows.  The barcoded libraries were pooled three to a chip for sequencing.  Base calling and primary analysis was performed using Torrent Suite 4.0.2

treatment_protocol: Conceptuses were flushed from the uterine horn with 10 ml of 10 mM PBS (pH 7.2). Conceptus tissue was transferred to a 1.5ml microcentrifuge tube and frozen in liquid nitrogen.

tag: day of pregnancy


title: PC3_AR-K2R_INPUT

city: Kuopio

first: Päivi

last: Sutinen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

library_source: genomic

data_processing:
The quality of raw reads was analyzed by FastQC
FASTX-toolkit was used for preprocessing (removal of artifacts, trimming (50bp), quality filtering and collapsing identical reads)
Reads were alignment Bowtie (0.12.7)(one mismatch and best alignment)
Analysis were done with HOMER software (4.2). Binding sites were determined with findpeaks (using -factor mode and input as a background).
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (find in both replicates)

molecule: genomic DNA

source_name: PC-3 cells

growth_protocol: PC-3 cells were grown in F-12 (10% FBS, 1% penicillin/streptomycin) under G418 selection (400 µg/ml).

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with 1 µg of antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols, as utilized at the Gene Core in EMBL, Heidelberg, Germany

treatment_protocol: PC-3 cells were growth 72h in transfection medium (5% stripped FBS in F-12) before treating 1 h with 10 nM R1881 or ethanol (vehicle).

tag: cell line

value: PC-3 prostate cancer cells

tag: antibody

tag: genotype/variation

value: SUMOylation-deficient AR


title: E3090

description: ribosomal depleted RNA


title: PC3_wtAR_R1881_rep1

value: rabbit antiserum against AR

tag: treatment

value: wild-type AR


title: F10

source_name: Male FSHD2 biopsy F10

value: Male

value: FSHD2 Muscle biopsy


title: F1

source_name: Male FSHD1 biopsy F1


title: F11

source_name: Male FSHD2 biopsy F11


title: C9

source_name: Female Control biopsy C9

value: Control Muscle biopsy


title: PC3_wtAR_EtOH

value: Ethanol


title: PC3_wtAR_INPUT


title: E3041

description: ribosomal depleted RNA


title: HEK293_AR-K2R_R1881_rep2

data_processing:
The quality of raw reads was analyzed by FastQC
FASTX-toolkit was used for preprocessing (removal of artifacts, quality filtering and collapsing identical reads)
Reads were alignment Bowtie (0.12.7)(one mismatch and best alignment)
Analysis were done with HOMER software (4.2). Binding sites were determined with findpeaks (using -factor mode and input as a background).
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (find in both replicates)

source_name: Isogenic HEK293 Cells

growth_protocol: Isogenic HEK293 cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with 1 µg of antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols, in Beijing Genomic institute (BGI)(HongKong, China).

treatment_protocol: Isogenic HEK293 cells were seeded at 10 cm plates and allowed to grow in steroid-depleted medium (2.5 %  charcoal stripped FBS in DMEM) 72 h and then the cells were exposured to 10 nM R1881 or EtOH (vehicle) for 40 min.

value: Human Embryonal Kidney Cells HEK-293

tag: treatment time

value: 40 min


title: C7

source_name: Female Control biopsy C7


title: C5

source_name: Male Control biopsy C5


title: C6

source_name: Female Control biopsy C6


title: HEK293_wtAR_R1881_rep2


title: HEK293_AR-K2R_R1881_rep1


title: C4

source_name: Male Control biopsy C4


title: HEK293_wtAR_R1881_rep1


title: Pol2_Ser2P_TTE-MBD2_ChIP-seq

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

data_processing:
Cluster generation and sequencing were performed using the Illumina GAIIx or HiSeq2000 genome analyzer. The 36 (GAIIx) or 43 bp tags (HiSeq2000) were mapped to the reference human genome hg19 (NCBI build 37), using the BWA allowing one mismatch. The image files were processed to extract DNA sequence data. Only uniquely mapped-reads were used for data analysis and visualization. The output data were converted to bam files for downstream analysis and bigWig (bw) files for viewing the data in the UCSC Genome Browser.
FASTQ sequence files were aligned using RMAPBS (Smith et al., 2009; Smith et al., in prep) allowing a maximum of 10 mismatches for efficient mapping of reads containing bisulfite converted unmethylated cytosines. Cytosine methylation levels were determined using the standard new pipeline within RMAPBS (Methpipe; Andrew Smith, in prep). In short, both mates of the paired-end sequencing were mapped separately by RMAPBS. If mated reads mapped within 300 bp, the reads were merged and included for analysis. Mated reads mapping with a distance of more than 300 bp were excluded from further analysis. Mated reads mapped within 300 bp, but mapping equally well on multiple positions on the genome, were discarded. If multiple mated reads mapped on exactly the same genomic coordinates, all but one (at random) were discarded. Symmetric cytosines (within a CpG context) on both forward and reverse strands were combined. Cytosine methylation level was called per individual C as: #C/(#C+#T).
Reads were aligned to hg19 using BWA. Details about aligner version and parameters used are stored in the headers of the BAM files. PCR duplicates were removed, therefore the final BAM files only contain uniquely mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig were generated by counting the number of sequence reads (directionally extended to a final 300 bp) per 10-bp genomic window. Methylation density represents methylation level per 50-bp genomic windows
Supplementary_files_format_and_content: Cytosine methylation levels within CpG context are present in the MCF7_CpG_methcounts.bed.gz
Supplementary_files_format_and_content: Peak-calling was performed with MACS 2.0 tool against a reference input sample from the cell line expressing TTE-MBD2

source_name: MCF-7 TTE-MBD2

extract_protocol:
Cells were fixed for 10 minutes at room temperature by the addition of formaldehyde to a final concentration of 1%, after which glycine was added to a concentration of 100 mM. Cells were then washed twice with PBS and collected into 2 ml of lysis buffer (150 mM NaCl, 20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, protease inhibitor [complete EDTA free, Roche, 04 693 132 001], 100 mM PMSF). The lysate was sonicated to an average of 300-500bp fragments The resulting sonicate was centrifuged at 4000×g for 5 minutes, an aliquot of 10% retained for input and the remaining material transferred to a fresh tube.
5-10 ng DNA was subjected to end repair using Klenow DNA polymerase, T4 ligase and T4 polynucleotide kinase (T4 PNK). A 3′ protruding A base was generated using Taq polymerase and NEXTflex adapters were ligated. The DNA was subjected to 4 cycles PCR amplification using Kappa polymerase and purified DNA was loaded on E-gel for size selection (300 bp). The DNA was isolated, further amplified by PCR and used for cluster generation on the HiSeq2000 genome analyzer

tag: genetic manipulation

value: MCF7 cell line has been stably trasfected with TTE-MBD2 construct.

tag: antibody/details

value: Anti-RNA polymerase II subunit B1 (phospho CTD Ser-2), clone 3E10, Millipore (Cat 04-1571)


title: C3

source_name: Male Control biopsy C3

tag: tissue


title: E3069

description: ribosomal depleted RNA


title: Rco_CCA

city: Saint Louis

first: Weixiong

last: Zhang

address: Campus Box 1045 One Brookings Drive

institute: Washington university in St Louis

description: small RNA-Seq

data_processing:
The raw sequence reads were first processed to remove reads with no 3' sequencing adaptor, of low quality, or shorter than 17 nt. The sequence adaptor trimming was done by an in-house program that recursively searches for the longest subsequence of the adaptor appearing within a sequence read. If a raw sequence read did not have a subsequence of the adaptor that was longer than 4 nt, it was considered to have no adaptor.
Genome_build: n/a
Supplementary_files_format_and_content: txt format. Content: 1st column is SEQUENCE;  2nd column is COUNT

organism: Ricinus communis

growth_protocol: Stem segments with three nodes of Cassava (Manihot esculenta Crantz) cultivar, were cut from 8-month-old plants, and inclined in 3-L pots filled with barren red soil: vermiculite (1:1, v/v), fertilized with Hoagland’s solution, to propagate and generate well-balanced seedlings. The solution was renewed with 300ml quarter-strength solution once a week. After 2 months of planting, the uniform seedlings were subjected to cold stress treatment. All plants were field grown at the Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, during April and June of natural conditions (11h light, 13h dark and 25°C during the day and 18°C at night).

extract_protocol: Total RNA of each sample was isolated individually, and then pooled with an equal amount from each sample into one for profiling. As a result, four mRNA libraries and four small-RNA libraries, corresponding to the conditions of CA, CCA,CS and NC, were constructed.

treatment_protocol: Three organs/tissues (folded leaf, fully expanded leaf and roots) of Cassava cultivar SC124 harvested at 6h, 24h and 5d for three cold treatments of CA, CCA and CS, for profiling genes at the stages of initial response, secondary response, and functional adaption to cold stresses.

value: Castor bean under stress acclimation Cold stress after cold acclimation (CCA)


title: HEK293_wtAR_EtOH


title: C2

source_name: Male Control biopsy C2


title: Patient 4 tumor 3

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Laser-microdissected squamous cell carcinoma

data_processing:
Single-end sequencing was performed for 36 cycles (patients 1 and 2) or 50 cycles (patients 3 and 4).  Basecalling was performed for all cycles for patients 1, 3 and 4 and for the first 35 cycles for patient 2.  Illumina CASAVA software version 1.6.0 (patients 1 and 2) or 1.7.0 (patients 3 and 4) was used for basecalling.  Reads that failed Illumina's chastity filter [brightest intensity / (brightest intensity + second brightest intensity) < 0.6 for at least two of the first 25 cycles] were automatically removed during preprocessing.
After chastity filtering, the first 35 bases of each read were aligned to the human genome (build hg19) using Bowtie v0.12.7 (the first base of reads from patient 1 was omitted during alignment due to a technical issue).  Only unique alignments were allowed, with up to two mismatches per read, with the command: 'bowtie -p 2 -a --best --strata -v 2 -m 1 -S --fullref -t'
Coverage estimates were computed by merging exons from all isoforms of each of 55,841 Ensembl Gene (ENSG) loci (Ensembl build 69) to create a single meta-transcript for each ENSG, and counting the number of reads falling in the exons of each meta-transcript using the BEDTools software suite.
Reads aligning to the mitochondrial genome were removed from further analysis. Reads per kilobase per million aligned reads (RPKM) were computed for each remaining ENSG in each sample by normalizing counts to the size of each meta-transcript and to the number of reads aligned to the nuclear genome in each sample.  RPKM values were seventh-root-transformed prior to analysis to produce an approximately normal distribution of (nonzero) gene expression values.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file including the number of reads (counts) overlapping each gene and sample.
Supplementary_files_format_and_content: Tab-delimited text file including RPKM values for each gene and sample.

source_name: Squamous cell carcinoma

extract_protocol:
Tissues were sectioned at a 7-micron thickness and mounted on regular uncharged glass slides for patients 1, 2, and 3, and on polyethylene napthalate (PEN) membrane slides (Leica) for patient 4, followed by H&E staining. LCM was performed using the Arcturus eIIx for patient 1 and 2, Zeiss PALM for patient 3, and Leica LMD7000 for patient 4. A tissue area of 800,000 to 1,200,000 μm2 was dissected and collected from each lesion.  RNA was extracted from laser-microdissected cells using the RNeasy Micro Kit (QIAGEN).
The cDNA was generated using the Ovation RNA-Seq System (NuGEN) for patients 1 and 2 and the 15 Ovation RNA-Seq V2 System (NuGEN) for patients 3 and 4. For patients 1 and 2, cDNA of ~200 bp was selected by gel purification. For patients 3 and 4, the cDNA was sheared to 140-180 bp using the Covaris focused-ultrasonicator with the following settings: duty cycle 10%; intensity 5; cycles per burst 200; total time 6 minutes.

tag: patient

value: Patient 4

tag: pathology

value: Tumor

value: Squamous cell carcinoma


title: Patient 4 tumor 2


title: Patient 4 premalignant 2

description: Laser-microdissected premalignant lesion

source_name: Premalignant lesion

value: Premalignant

value: Premalignant lesion


title: Patient 4 tumor 1


title: Rco_NC

description: small RNA-Seq

source_name: folded leaf, fully expanded leaf and roots

value: Castor bean under normal condition (NC)


title: Patient 4 premalignant 1


title: C8

source_name: Female Control biopsy C8

value: Female


title: miRNA-seq_R-NSCP6

city: Los Angeles

first: Yuqi

last: Zhao

state: CA

address: 2000 Terasaki Life Sciences Bldg 610 Charles E. Young Drive East

department: Department of Integrative Biology and Physiology

institute: University of California, Los Angeles

description: Supplementary S2.xls

data_processing:
RNA-seq reads were aligned to the rheMac3 genome assembly using Bowtie 0.12.8.0
Tophat 2.0.5 was used to analyze the mapping results to identify splice junctions
Cufflinks 2.0.2 were used to assemble transcripts, estimate expression abundances, and test for differentially expressed genes between stages
miRNA-seq reads were aligned to rhesus rheMac3 and miRBase (version 19) using miRDeep2
Alternative Splicing analyses was performed using MATS software (version 3.0.7.beta)
Genome_build: rheMac3
Supplementary_files_format_and_content: Microsoft Excel files, with rows representing genes and columns representing stages. The values are FPKM values in mRNA profile (Supplementary S1.xls) and the values are read counts in miRNA-seq (Supplementary S2.xls).

organism: Macaca mulatta

source_name: R-NSCs at late passages

growth_protocol: Rhesus monkey ESCs (line IVF3.2) were cultured on feeder cells of mitotically inactivated mouse embryonic fibroblasts (MEFs) as described previously. Embryoid bodies (EBs) differentiation was employed to induce neural differentiation. Briefly, rESC colonies were transferred onto tissue culture dishes coated with 1% agar and differentiated in ESC culture medium depleted of bFGF to induce EB differentiation. EBs were then transferred onto ECM-coated (10 μg/cm2, Sigma-Aldrich) tissue culture dishes to spread and propagate in DMEM/F12 medium (Gibco) supplied with ITS (Sigma-Aldrich), 2.5 ug/mL fibronectin (Millipore), 60 µM putrescine (Sigma-Aldrich), and 20 ng/ml bFGF. Neural tube-like structures could be observed in EB outgrowth and rosette-like clusters were then manually separated and expanded according to the protocol described by Elkabetz et al. with minor modifications. In brief, rosette clusters were replaced on culture dishes pre-coated with 15 µg/mL polyornithine plus 1 µg/mL laminin (Po/Lam) (Sigma-Aldrich) in N2 medium supplemented with SHH (200 ng/mL; R&D), FGF8 (100 ng/mL; Sigma-Aldrich), ascorbic acid (0.2 mM; Sigma-Aldrich), and brain-derived neurotrophic factor (BDNF, 20 ng/mL; R&D). The first passage of rosettes culture was defined as R-NSCP1. Cells were passed at density of 100–400 × 103 cells/cm2 when the growth reached 80% confluency. R-NSCs were propagated in Po/Lam culture dishes in N2 medium with 0.2 mM ascorbic acid, 20 ng/mL BDNF, 500 ng/mL SHH, 500 ng/mL Dll4 (R&D) and 500 ng/mL Jagged-1 (R&D). Under this culture condition, rosette structure can be maintained for up to five generations. At the 6th generation, the rosette structure was no longer visible and the cells were defined as R-NSCP6. Neural progenitor cells (NPCs) were derived from R-NSCs with extended culture on Po/Lam culture dishes in N2 medium plus 0.2 mM ascorbic acid, 20 ng/mL BDNF, 20 ng/mL FGF2, and 20 ng/mL EGF for more than 100 days.

extract_protocol:
According to the manufacturer’s instructions (illumina), mRNA was purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces. The cleaved RNA fragments were converted to the first strand cDNA followed by generation of double strand cDNAs. These cDNA fragments went through end repair course by adding a single ‘A’ base as well as the adapter ligation. For miRNA sequencing, total RNA was ligated to a pair of adaptors at the 5’ and 3’ends according to the manufacturer’s instructions (Illumina). RNA molecules were converted to cDNA and amplified by RT-PCR using adaptor primers.
The libraries prepared from samples of ESCs, R-NSCP1, R-NSCP6, and NPCs were used for paired-end mRNA sequencing by Illumina HiSeq 2000 and single-end miRNA sequencing by  Illumina HiSeq 2000.

tag: developmental stage

value: The sixth passage of rosettes culture

tag: genotype

value: wild type


title: miRNA-seq_ESC

description: Supplementary S2.xls

source_name: embryonic stem cells

value: embryonic stem cell


title: miRNA-seq_NPC

description: Supplementary S2.xls

source_name: Neural progenitor cells

value: Neural progenitor cells


title: PC3_wtAR_R1881_rep2

source_name: PC-3 cells

value: PC-3 prostate cancer cells

value: rabbit antiserum against AR

value: wild-type AR


title: miRNA-seq_R-NSCP1

description: Supplementary S2.xls

source_name: R-NSCs at early passage

value: The first passage of rosettes culture


title: Patient 3 tumor 3

value: Patient 3


title: Patient 3 tumor 1


title: Patient 3 tumor 2


title: Patient 4 normal 1

description: Laser-microdissected normal basal cells

source_name: Normal basal cells

value: Normal

tag: cell type

value: Normal basal cells


title: Patient 3 premalignant 2


title: Patient 3 premalignant 1


title: C1

source_name: Male Control biopsy C1

value: Male

value: Control Muscle biopsy


title: Patient 3 normal 1

description: Laser-microdissected normal basal cells


title: mRNA-seq_R-NSCP1

description: Supplementary S1.xls


title: mRNA-seq_NPC

description: Supplementary S1.xls


title: mRNA-seq_R-NSCP6

description: Supplementary S1.xls


title: mRNA-seq_ESC

description: Supplementary S1.xls


title: Patient 4 normal 2

description: Laser-microdissected normal basal cells

value: Patient 4


title: ICM29_PLntr_1

status: Public on Jul 02 2014

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
Sample name: ICM29_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG

data_processing:
Base calling was done using CASAVA versions 1.6 - 1.8.2.
The data was processed as described in Brown et al. (2013, Front Genet, 4:145) using a curated miRNA (Farazi et al. 2011, 71:4443) and other non-coding and coding RNA transcriptomes.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files contain raw, i.e. not-normalized or transformed, miRNA counts based on unique miRNA sequences, or based on precursor clusters and sequence families.

source_name: stable heart failure-ICM-plasma-conservative treatment

extract_protocol:
Total RNA was isolated using a modified TRIzol protocol including another acidic phenol chloroform extraction followed by ethanol precipitation; the myocardial samples were additionally treated by DNase I treatment and proteinase K digestion in the presence of 0.5 % SDS, and recovered by two ethanol precipitations. Total RNA from liquid specimen was isolated using TRIzol LS, followed by a 2-propanol precipitation in the presence of glycogen, a proteinase K digestion (f.c. 100 µg/ml in 0.5 % SDS for 20 min at 42 degrees C), another acidic phenol-chloroform extraction, and two ethanol precipitations.
The small RNA libraries for the solid tissue samples were prepared using the protocol described in Hafner et al. (2008, 44:3, 2012, 58:164). The libraries for for the serum and plasma samples had the following modifications: 1) the amount of the 10 spiked-in synthetic calibrator oligoribonucleotides was reduced from 0.5 fmol each per 2 µg total RNA input to 0.005 fmol each, 2) the synthetic P32-labeled 19-nt and 24-/35-nt ssRNAs used for size selection were not spiked-into the samples. Note: no calibrator oligoribonucleotides were spiked-in to library 8. The sequences of the 10 used calibrator oligoribonucleotides can be obtained from Hafner et al. 2012 (Methods, 58:164).

tag: age

tag: race

value: Caucasian

value: Plasma

tag: disease

value: Ischemic Cardiomyopathy

tag: heart failure onset

tag: nyha

tag: ejection fraction

tag: lvad status

value: No LVAD

tag: lvad device

tag: days lvad

tag: pacemaker


title: ICM30_PLntr_1

description:
Sample name: ICM30_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG

tag: gender


title: ICM33_PLntr_1

description:
Sample name: ICM33_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG

value: Female

tag: tissue


title: ICM34_PLntr_1

description:
Sample name: ICM34_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG


title: ICM31_PLntr_1

description:
Sample name: ICM31_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG


title: MF

city: LIN AN

first: ZHENGJIA

last: WANG

address: 88 NORTH CIRCLE ROAD

country: China

institute: ZHEJIANG A & F UNIVERSITY

description: small RNA

data_processing:
Small clean RNAs were mapped to the genome of hickory sequenced by 454 (unpublished data) and to Populus trichocarpa genome (http://genome.jgi-psf.org/Poptr1_1/) using SOAP software
Perfect sRNA matches were retained for further analysis. Sequences matching noncoding RNAs included rRNAs, tRNAs, snRNAs, and snoRNAs in the Rfam (http://www.sanger.ac.uk/Software/Rfam) and NCBI GenBank databases (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi) were discarded.
Conserved miRNAs were obtained by BLAST searches, allowing two mismatches, of miRBase 17.0 (http://www.mirbase.org/index.shtml) and were confirmed by predicting the characteristic secondary structures of miRNAs using RNAfold (http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.8.1.tar.gz). Mireap software (https://sourceforge.net/projects/mireap/) was used to predict novel miRNAs from the unknown sRNAs in our sequenced genome of hickory.
Concentrating on the selected miRNA sequences, we found that some sRNAs perfectly matched the selected miRNA sequences and were trimmed one or more nucleotides at the 3′ or 5′ ends; these were considered to be truncated miRNAs, the intermediates of miRNA degradation. Moreover, we observed that one or more nucleotides at 3′ or 5′ ends, based on the precursor sequences, were added to the sRNAs that perfectly matched the miRNA sequences. The degradation products of these sRNAs were either mature or truncated miRNAs. Therefore, these sRNAs were also used to analyze the degradation of miRNAs.
Modifications of miRNA sequences by 3′ nucleotide additions were called isomiRs. We found that to the sRNAs that perfectly matched mature miRNAs were added one or more nucleotides at the 3′ end; these were considered to be isomiRs. There were two kinds of isomiRs, nontemplated and templated, depending on whether or not they were based on the sequences of miRNA precursors. These isomiRs were often appended with A, G, C, or U (e.g., miR156b-A or isomiR-A).

organism: Populus trichocarpa

source_name: female flower

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

value: flower bud

value: female


title: ICM25_PLntr_1

description:
Sample name: ICM25_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG

value: African American


title: ICM28_PLntr_1

description:
Sample name: ICM28_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG


title: ICM27_PLntr_1

description:
Sample name: ICM27_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG


title: ICM26_PLntr_1

description:
Sample name: ICM26_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG

value: Asian


title: ICM24_PL3mo_1

description:
Sample name: ICM24_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TATCA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TATCATCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-ICM-plasma-3 months LVAD treatment

value: IV

value: 3 months LVAD support

value: HeartMate II

value: Yes


title: ICM22_PLimp_1

description:
Sample name: ICM22_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-ICM-plasma-at LVAD implantation


title: ICM23_PLimp_1

description:
Sample name: ICM23_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG


title: ICM23_PL6mo_1

description:
Sample name: ICM23_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-ICM-plasma-6 months LVAD treatment

value: 6 months LVAD support


title: AF

description: small RNA


title: ICM22_PL3mo_1

description:
Sample name: ICM22_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG

value: Male


title: ICM21_PL3mo_1

description:
Sample name: ICM21_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG

value: HeartWare


title: ICM21_PLimp_1

description:
Sample name: ICM21_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG


title: ICM19_LVimp_1

description:
Sample name: ICM19_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG

source_name: failing ICM left-ventricular myocardium, before LVAD support

value: Cardiac Muscle


title: ICM20_LVimp_1

description:
Sample name: ICM20_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG

value: Caucasian


title: ICM19_LVexp_1

description:
Sample name: ICM19_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG

source_name: failing ICM left-ventricular myocardium, after LVAD support

value: Explantation


title: ICM18_PLimp_1

description:
Sample name: ICM18_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG

value: Plasma

value: Ischemic Cardiomyopathy

value: No


title: ICM18_SRexp_1

description:
Sample name: ICM18_SRexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-ICM-serum-at LVAD explantation for heart transplantation

value: Serum


title: ICM18_SRimp_1

description:
Sample name: ICM18_SRimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-ICM-serum-at LVAD implantation

value: No LVAD


title: ICM24_PLimp_1

description:
Sample name: ICM24_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG


title: HEK293_AR-K2R_EtOH

source_name: Isogenic HEK293 Cells

tag: cell line

value: Human Embryonal Kidney Cells HEK-293

tag: antibody

value: rabbit antiserum against AR

tag: treatment

value: Ethanol

tag: treatment time

value: 40 min

tag: genotype/variation

value: SUMOylation-deficient AR


title: ICM18_PLexp_1

description:
Sample name: ICM18_PLexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-ICM-plasma-at LVAD explantation for heart transplantation

tag: age

value: IV

value: HeartMate II

value: Yes


title: ICM17_LVimp_1

description:
Sample name: ICM17_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG

value: Male

tag: race


title: ICM17_LVexp_1

description:
Sample name: ICM17_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG

value: Cardiac Muscle

tag: disease


title: ICM17_PLimp_1

description:
Sample name: ICM17_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG

value: Caucasian

tag: heart failure onset


title: ICM17_PLexp_1

description:
Sample name: ICM17_PLexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG

tag: nyha

value: Explantation


title: ICM16_PL3mo_1

description:
Sample name: ICM16_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TATCA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TATCATCGTATGCCGTCTTCTGCTTG

value: Plasma

value: III

tag: ejection fraction

value: 3 months LVAD support


title: ICM16_PLimp_1

description:
Sample name: ICM16_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG

value: Ischemic Cardiomyopathy

tag: lvad status


title: ICM15_PL6mo_1

description:
Sample name: ICM15_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG

value: 6 months LVAD support

tag: lvad device


title: ICM13_PLimp_1

description:
Sample name: ICM13_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG

value: No LVAD

tag: days lvad


title: ICM14_PLimp_1

description:
Sample name: ICM14_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG

value: Female

tag: pacemaker


title: ICM15_LVimp_1

description:
Sample name: ICM15_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG

tag: gender


title: ICM14_PL6mo_1

description:
Sample name: ICM14_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG

tag: tissue


title: ICM13_PL6mo_1

description:
Sample name: ICM13_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG


title: ICM12_PLimp_1

description:
Sample name: ICM12_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG


title: ICM12_PL3mo_1

description:
Sample name: ICM12_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG


title: ICM12_PL6mo_1

description:
Sample name: ICM12_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG


title: ICM11_LVimp_1

description:
Sample name: ICM11_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TTACA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTACATCGTATGCCGTCTTCTGCTTG

value: Asian


title: ICM09_PLimp_1

description:
Sample name: ICM09_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG


title: ICM09_PL3mo_1

description:
Sample name: ICM09_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG


title: ICM17_SRimp_1

description:
Sample name: ICM17_SRimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG

value: Serum


title: ICM17_PLimp_2

description:
Sample name: ICM17_PLimp_2
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG


title: ICM17_SRexp_1

description:
Sample name: ICM17_SRexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG


title: ICM15_PLimp_1

description:
Sample name: ICM15_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG


title: ICM07_SRimp_1

description:
Sample name: ICM07_SRimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG


title: ICM08_PL6mo_1

description:
Sample name: ICM08_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG


title: ICM07_PLimp_1

description:
Sample name: ICM07_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG


title: ICM07_PLimp_2

description:
Sample name: ICM07_PLimp_2
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG


title: ICM07_SRexp_1

description:
Sample name: ICM07_SRexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG


title: ICM06_SRimp_1

description:
Sample name: ICM06_SRimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG

value: II-III


title: ICM07_LVexp_1

description:
Sample name: ICM07_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG


title: ICM06_SRexp_1

description:
Sample name: ICM06_SRexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG


title: ICM06_PLimp_1

description:
Sample name: ICM06_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG


title: ICM06_PLexp_1

description:
Sample name: ICM06_PLexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG


title: ICM05_LVimp_1

description:
Sample name: ICM05_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG


title: ICM05_LVexp_1

description:
Sample name: ICM05_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG


title: ICM08_PLimp_1

description:
Sample name: ICM08_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG

value: IV


title: ICM11_LVexp_1

description:
Sample name: ICM11_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG

value: HeartMate II


title: ICM32_PLntr_1

description:
Sample name: ICM32_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG


title: ICM03_PLimp_1

description:
Sample name: ICM03_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG

value: African American

value: Yes


title: HUV02_PCntr_1

description:
Sample name: HUV02_PCntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 16
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG

source_name: human umbilical vein endothelial cell

value: Primary Cells


title: HUV01_PCntr_1

description:
Sample name: HUV01_PCntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 16
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG


title: CAGE Rrp40 rep 3

city: Copenhagen N

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

description: For the 5' end, an extra G in position 10 of the reads, right after the barcode, needs to be trimmed. This is due to an artifact in the reverse transcription of the capped G. For the 3'end, the last 8 nt also needs to be trimmed due to 3' end adaptors.

data_processing:
CAGE: basecalling by CASAVA version 1.8.2. The first 11 nt from 5'end and the last 6 nt from 3'end are trimmed off.  All the reads are then filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50 and mapped to hg19 by bowtie version 0.12.7 using --strata --best -k 10. Only 5'end of uniquely mapped reads are used in the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: CAGE bed files contain positions of 5' ends of unique locations of CAGE tags and the number of CAGE tags at that position (score column).

source_name: HeLa

growth_protocol: HeLa cells grown in DMEM medium supplemented with 10% fetal bovine serum at 37°C and 5% CO2.

extract_protocol:
Purelink (Ambion)
CAGE (PMID: 21938627)

treatment_protocol: 22nM siRNA transfection (double hit)

tag: barcode

value: GATCAGCAG

value: Rrp40 knock down (exosome)

tag: cell line

value: HeLa


title: CAGE Rrp40 rep 1

value: ATGCAGCAG

tag: treatment


title: DCM26_PLntr_1

description:
Sample name: DCM26_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG

source_name: stable heart failure-DCM-plasma-conservative treatment

value: Male

value: Hispanic

value: Plasma

value: Dilated Cardiomyopathy


title: CAGE Rrp40 rep 2


title: DCM24_PLntr_1

description:
Sample name: DCM24_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG

value: Female

value: No LVAD


title: DCM25_PLntr_1

description:
Sample name: DCM25_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG

value: Caucasian


title: ICM07_PL3mo_1

description:
Sample name: ICM07_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG

value: Ischemic Cardiomyopathy

value: III

value: 3 months LVAD support


title: CAGE Mtr4 rep 3

value: Mtr4 knock down (exosome)


title: DCM23_PLntr_1

description:
Sample name: DCM23_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG

value: African American


title: ICM07_LVimp_2

description:
Sample name: ICM07_LVimp_2
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG

value: Cardiac Muscle

value: HeartMate II

value: Yes


title: ICM07_PLexp_1

description:
Sample name: ICM07_PLexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG

value: Explantation


title: CAGE Mtr4 rep 2

value: ATGCAGCAG

value: HeLa


title: DCM22_PLimp_1

description:
Sample name: DCM22_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-DCM-plasma-at LVAD implantation

value: Male


title: DCM22_PL6mo_1

description:
Sample name: DCM22_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-DCM-plasma-6 months LVAD treatment

value: Plasma

value: 6 months LVAD support


title: DCM22_PL3mo_1

description:
Sample name: DCM22_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-DCM-plasma-3 months LVAD treatment

value: Dilated Cardiomyopathy


title: CAGE Mtr4 rep 1


title: CAGE Egfp rep 3

value: GATCAGCAG

value: Egfp knock down (control)


title: DCM21_LVexp_1

description:
Sample name: DCM21_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG

source_name: failing DCM left-ventricular myocardium, after LVAD support

value: Caucasian


title: DCM20_LVimp_1

description:
Sample name: DCM20_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG

source_name: failing DCM left-ventricular myocardium, before LVAD support

value: Female

value: No LVAD


title: DCM21_LVimp_1

description:
Sample name: DCM21_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG


title: ICM03_PL6mo_1

description:
Sample name: ICM03_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG

value: Ischemic Cardiomyopathy

value: III


title: DCM20_LVexp_1

description:
Sample name: DCM20_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG

value: Cardiac Muscle


title: DCM19_PLimp_1

description:
Sample name: DCM19_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG

value: HeartMate II


title: CAGE Egfp rep 1

description: For the 5' end, an extra G in position 10 of the reads, right after the barcode, needs to be trimmed. This is due to an artifact in the reverse transcription of the capped G. For the 3'end, the last 8 nt also needs to be trimmed due to 3' end adaptors.


title: CAGE Egfp rep 2


title: DCM19_LVimp_1

description:
Sample name: DCM19_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG

value: Yes


title: DCM18_LVimp_1

description:
Sample name: DCM18_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG


title: DCM17_LVimp_1

description:
Sample name: DCM17_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG


title: RBC02_PCntr_1

description:
Sample name: RBC02_PCntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 18
Processed data published in PMID 23440203.
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG

source_name: red blood cells

value: Primary Cells


title: DCM16_SRimp_1

description:
Sample name: DCM16_SRimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-DCM-serum-at LVAD implantation

value: Serum

value: III-IV


title: DCM16_SRexp_1

description:
Sample name: DCM16_SRexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-DCM-serum-at LVAD explantation for heart transplantation

value: Male

value: Explantation


title: DCM19_PL6mo_1

description:
Sample name: DCM19_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG

value: Plasma

value: 6 months LVAD support


title: DCM16_PLimp_1

description:
Sample name: DCM16_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG

value: Dilated Cardiomyopathy


title: DCM16_LVimp_1

description:
Sample name: DCM16_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG


title: DCM16_PLexp_1

description:
Sample name: DCM16_PLexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG

source_name: advanced heart failure-DCM-plasma-at LVAD explantation for heart transplantation


title: RBC01_PCntr_1

description:
Sample name: RBC01_PCntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 18
Processed data published in PMID 23440203.
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG


title: DCM16_LVexp_1

description:
Sample name: DCM16_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG


title: DCM15_LVimp_1

description:
Sample name: DCM15_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG


title: PMC01_PCntr_1

description:
Sample name: PMC01_PCntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 17
Processed data published in PMID 23131772.
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG

source_name: peripheral blood mononucleated cells


title: ICM13_LVimp_1

description:
Sample name: ICM13_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG

source_name: failing ICM left-ventricular myocardium, before LVAD support


title: DCM14_PLimp_1

description:
Sample name: DCM14_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG

value: IV

value: HeartWare


title: ICM10_LVimp_1

description:
Sample name: ICM10_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG

value: Caucasian


title: ICM08_LVimp_1

description:
Sample name: ICM08_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG

value: No LVAD


title: ICM07_SMntr_1

description:
Sample name: ICM07_SMntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG

source_name: skeletal muscle, postnatal

value: Skeletal Muscle


title: DCM12_PLimp_1

description:
Sample name: DCM12_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG


title: DCM13_LVimp_1

description:
Sample name: DCM13_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG

value: African American


title: DCM13_PL3mo_1

description:
Sample name: DCM13_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG

value: 3 months LVAD support


title: ICM07_LVimp_1

description:
Sample name: ICM07_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG

value: Cardiac Muscle

value: Ischemic Cardiomyopathy

value: HeartMate II


title: DCM12_PL6mo_1

description:
Sample name: DCM12_PL6mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG

value: Yes


title: DCM12_LVimp_1

description:
Sample name: DCM12_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG


title: ICM04_LVimp_1

description:
Sample name: ICM04_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG


title: DCM11_LVimp_1

description:
Sample name: DCM11_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG

value: Hispanic


title: ICM02_LVimp_1

description:
Sample name: ICM02_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG

value: Male


title: DCM10_LVimp_1

description:
Sample name: DCM10_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG


title: ICM01_LVimp_1

description:
Sample name: ICM01_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 1
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG

value: HeartMate I


title: DCM14_LVimp_1

description:
Sample name: DCM14_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TATCA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TATCATCGTATGCCGTCTTCTGCTTG

value: Heartware


title: ICM02_LVexp_1

description:
Sample name: ICM02_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG

source_name: failing ICM left-ventricular myocardium, after LVAD support

value: Explantation


title: DCM06_SRexp_1

description:
Sample name: DCM06_SRexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG

value: Serum

value: Dilated Cardiomyopathy

value: III


title: DCM06_SRimp_1

description:
Sample name: DCM06_SRimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG

value: Caucasian


title: DCM13_PLimp_1

description:
Sample name: DCM13_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG

value: Plasma

value: IV

value: No LVAD


title: DCM06_LVexp_1

description:
Sample name: DCM06_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TATCA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TATCATCGTATGCCGTCTTCTGCTTG


title: DCM08_LVimp_1

description:
Sample name: DCM08_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG

value: African American


title: FET06_SMntr_1

description:
Sample name: FET06_SMntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 14
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG

source_name: skeletal muscle, fetal

value: Skeletal Muscle


title: DCM07_LVimp_1

description:
Sample name: DCM07_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG

value: Cardiac Muscle


title: DCM06_PLimp_1

description:
Sample name: DCM06_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG

value: HeartMate II


title: DCM06_LVimp_1

description:
Sample name: DCM06_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG

value: Yes


title: DCM09_LVimp_1

description:
Sample name: DCM09_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG

value: Hispanic


title: ICM01_LVexp_1

description:
Sample name: ICM01_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 1
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG

value: Male

value: Ischemic Cardiomyopathy


title: DCM06_PLexp_1

description:
Sample name: DCM06_PLexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG


title: FET05_LVntr_2

description:
Sample name: FET05_LVntr_2
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 13
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG

source_name: left-ventricular myocardium, fetal

value: Female


title: DCM05_PLimp_1

description:
Sample name: DCM05_PLimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG

value: II-III


title: DCM05_PLexp_1

description:
Sample name: DCM05_PLexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TTACA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTACATCGTATGCCGTCTTCTGCTTG

value: Explantation


title: DCM05_PLimp_2

description:
Sample name: DCM05_PLimp_2
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG

value: Dilated Cardiomyopathy


title: DCM05_SRimp_1

description:
Sample name: DCM05_SRimp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG

value: Serum


title: FET05_LVntr_1

description:
Sample name: FET05_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 1
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG

value: No


title: DCM05_SRexp_1

description:
Sample name: DCM05_SRexp_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TTACA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTACATCGTATGCCGTCTTCTGCTTG


title: FET04_LVntr_1

description:
Sample name: FET04_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG


title: DCM05_PL3mo_1

description:
Sample name: DCM05_PL3mo_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG

value: Plasma

value: 3 months LVAD support


title: DCM05_LVimp_1

description:
Sample name: DCM05_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG

value: No LVAD


title: FET03_SMntr_1

description:
Sample name: FET03_SMntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 14
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG


title: DCM05_LVexp_1

description:
Sample name: DCM05_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TATCA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TATCATCGTATGCCGTCTTCTGCTTG

value: African American


title: FET03_LVntr_1

description:
Sample name: FET03_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TTACA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTACATCGTATGCCGTCTTCTGCTTG


title: FET02_LVntr_2

description:
Sample name: FET02_LVntr_2
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 14
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG


title: DCM04_LVimp_2

description:
Sample name: DCM04_LVimp_2
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG


title: CTL22_APntr_1

description:
Sample name: CTL22_APntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 15
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG

source_name: adipose tissue, postnatal

value: Connective Tissue


title: CTL26_SPntr_1

description:
Sample name: CTL26_SPntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 15
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG

source_name: spleen, postnatal


title: CTL24_HPntr_1

description:
Sample name: CTL24_HPntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 15
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG

source_name: liver, postnatal

value: Epithelial


title: CTL23_BRntr_1

description:
Sample name: CTL23_BRntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 15
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG

source_name: brain tissue, postnatal

value: Neuronal Tissue


title: CTL25_SKntr_1

description:
Sample name: CTL25_SKntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 15
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG

source_name: skin, postnatal

value: Yes


title: CTL21_PLntr_2

description:
Sample name: CTL21_PLntr_2
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TATCA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TATCATCGTATGCCGTCTTCTGCTTG

source_name: healthy control-plasma-untreated

value: Hispanic


title: DCM04_SMntr_1

description:
Sample name: DCM04_SMntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG

value: Male

value: Skeletal Muscle

value: III-IV

value: HeartMate II


title: FET02_LVntr_1

description:
Sample name: FET02_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 14
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG

value: Cardiac Muscle


title: CTL19_PLntr_1

description:
Sample name: CTL19_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TTACA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTACATCGTATGCCGTCTTCTGCTTG


title: FET01_LVntr_1

description:
Sample name: FET01_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 13
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG


title: CTL20_PLntr_1

description:
Sample name: CTL20_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG

value: Caucasian


title: CTL19_PLntr_2

description:
Sample name: CTL19_PLntr_2
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG


title: CTL18_PLntr_1

description:
Sample name: CTL18_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG


title: CTL17_PLntr_2

description:
Sample name: CTL17_PLntr_2
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG


title: CTL16_PLntr_1

description:
Sample name: CTL16_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG


title: DCM04_LVimp_1

description:
Sample name: DCM04_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG

source_name: failing DCM left-ventricular myocardium, before LVAD support

value: Dilated Cardiomyopathy


title: DCM03_LVexp_1

description:
Sample name: DCM03_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 1
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG

source_name: failing DCM left-ventricular myocardium, after LVAD support

value: Explantation

value: HeartMate I


title: CTL15_PLntr_2

description:
Sample name: CTL15_PLntr_2
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 10
barcode: TTACA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTACATCGTATGCCGTCTTCTGCTTG

value: Plasma


title: CTL17_PLntr_1

description:
Sample name: CTL17_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG

value: No LVAD


title: CTL15_PLntr_1

description:
Sample name: CTL15_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG


title: DCM02_LVimp_1

description:
Sample name: DCM02_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG


title: DCM03_LVimp_1

description:
Sample name: DCM03_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 1
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG


title: CTL14_PLntr_1

description:
Sample name: CTL14_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 9
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG


title: CTL13_PLntr_1

description:
Sample name: CTL13_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 12
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG

value: Female


title: DCM02_LVexp_1

description:
Sample name: DCM02_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG


title: CTL21_PLntr_1

description:
Sample name: CTL21_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 11
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG


title: DCM01_LVimp_1

description:
Sample name: DCM01_LVimp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG

value: African American


title: DCM01_LVexp_1

description:
Sample name: DCM01_LVexp_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 3
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG


title: CTL12_PLntr_1

description:
Sample name: CTL12_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG


title: CTL12_SRntr_1

description:
Sample name: CTL12_SRntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG

source_name: healthy control-serum-untreated

value: Serum


title: CTL11_SRntr_1

description:
Sample name: CTL11_SRntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG


title: CTL04_LVntr_1

description:
Sample name: CTL04_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TTACA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTACATCGTATGCCGTCTTCTGCTTG

source_name: nonfailing left-ventricular myocardium, postnatal