title: LS411N_2


title: LS1034_3

status: Public on Sep 01 2013

type: RNA

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

country: Germany

institute: University Medical Center Göttingen

hyb_protocol: Hybridization was carried out for 20 hours.

scan_protocol: Slides were washed and scanned using an Agilent G2505B scanner.

data_processing: Raw data were extracted using the Feature Extraction software version 9.1 (Agilent Technologies). Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

molecule: total RNA

organism: Homo sapiens

source_name: human colorectal cancer cell line

label_protocol: 500 ng of total RNA and Spike-In were labeled by ligation to Cy3-conjugated 3´, 5´-cytidine-bisphosphate using T4 RNA ligase. Spin columns were used for desalting (BioRad, Hercules, CA, USA).

growth_protocol: Cell lines were cultured in their recommended medium (Invitrogen, Karlsruhe, Germany), supplemented with fetal bovine serum (Pan, Aidenbach, Germany) and 2 mM L-glutamine (BioWhittaker, Verviers, Belgium).

extract_protocol: For each cell line, total RNA was isolated from three different passages (passage four to six, at 60-70% confluence) using the miRNeasy Mini kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Cells are untreated. Sixty-nine hours after transfection, cells were exposed to 3µM of 5-FU and a single dose of 2 Gy of X-rays, and cell survival was determined by a standard colony formation assay.

tag: cell line


title: PBMC_232_day-7

status: Public on Apr 10 2014

city: Bethesda

first: Yuri

last: Kotliarov

state: MD

address: 4 Memorial Dr., room 134

department: CHI

country: USA

institute: NHLBI

description:
232_day-7
Gene expression data from PBMC extracted from individual 232 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

hyb_protocol: Labeled cDNA were hybridized to Human 1.0 ST GeneChip arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), according to the respective manufacturers' instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The raw intensities of gene probesets in the CEL files were processed using Affymetrix Power Tools. The apt-probeset_summarize script was used for background correction and normalization (RMA with sketch, quantile normalization). The Bioconductor package arrayQualityMetrics was used to assess the quality of the microarray data.

label: biotin

source_name: Individual 232 at day-7

label_protocol: Fragmented single-stranded sense cDNA were terminally labeled with biotin according to the standard Affymetrix protocol.

growth_protocol: Blood specimens were collected in heparinized syringes and peripheral blood mononuclear cells (PBMC) were isolated using Leucosep tubes with Ficoll-Paque Plus density gradient media and centrifugation. Fresh isolated PBMC were directly lysed in 700ul of Qiazol and stored at -80C till isolation.

extract_protocol: Total RNA was isolated from 1e7 freshly isolated PBMC using miRNeasy kit (Qiagen) according to the manufacturer’s instructions and eluted in 40ul of elution buffer with the addition of 1ul of RNase inhibitor (Invitrogen).

treatment_protocol: Individuals were vaccinated with the 2009 Fluvirin seasonal influenza (Novartis), and H1N1 pandemic (Sanofi-Aventis) vaccines, both without adjuvant.

tag: individual id

tag: tissue

tag: gender

value: female

tag: age

tag: ethnicty

value: Asain

tag: sample collection time

value: 7 days prior to vaccination (day-7)


title: SW403_2


title: LS513_3


title: LS1034_1


title: HT29_3


title: HT29_1


title: HT29_2


title: col0

status: Public on Aug 16 2013

type: SRA

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

description: smRNA from wild-type Col-0 plants

library_source: transcriptomic

data_processing: Raw smRNA-seq reads were first trimmed for 3'-adapters using the VectorStrip program that is part of the EBI EMBOSS package. At least 8 nt of the adapter sequences were required for successful trimming; the remaining untrimmed reads were discarded. Successfully trimmed reads were reduced to non-redundant sequences (NR-seq) and mapped to Arabidopsis genome (TAIR9 assembly) as described previously (Zheng et al., 2010), with maximum 8% mismatches allowed. All the clone-abundance and alignment information were loaded into local MySQL databases for further queries.

organism: Arabidopsis thaliana

source_name: unopened flower buds

growth_protocol: Plants were grown on soil in 16 hours of light and 8 hours of dark

extract_protocol: Briefly, smRNA-seq libraries were produced using the Small RNA Sample Prep v1.5 kit (Illumina, San Diego, CA) as per manufacturerâs instruction.

tag: genotype

value: wild-type

tag: ecotype


title: Caco2_3


title: Caco2_2


title: dcp5

description: smRNA from dcp5 mutant plants


title: Caco2_1


title: VSV_Ago2

status: Public on Jan 31 2013

description:
vsiRNA from VSV-infected Ago2 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

data_processing: Sequence information was extracted from the image files with the Illumina base calling software package (GAPipeline version 1.4). Prior to alignment of the smRNA reads, 'vectorstip' in the EMBOSS package was used to identify the first eight bases of the 3' adaptor sequence, and the sequencing read was truncated up to the junction with the adaptor sequence. No further analysis was performed on reads that did not contain adaptor sequence, as those reads lacking an adaptor cannot be precisely sized. The smRNA reads were then reduced to a list of only non-redundant (NR) sequences to minimize the computational requirement in all following procedures. It is of note that the number of times each smRNA was sequenced is maintained during this reduction step. The NR smRNA reads with perfect matches of length 15-29 nt were aligned to corresponding virus genomes and parsed using in-house Perl scripts to obtain the genomic location of smRNAs on the viral genome.

organism: Drosophila melanogaster

source_name: VSV-infected Ago2 knockdown dl1 cells

growth_protocol: Drosophila DL1 cells were grown and maintained as previously described (Cherry S & Perrimon N, 2004).  RVFV strain MP12 was grown in Vero cells (Caplen H et.al., 1985). VSV-eGFP (gift from J. Rose) was grown in BHK cells as described (Ramsburg E et.al., 2005). DCV was grown and purified as described (Cherry S & Perrimon N, 2004). Vaccinia strain vPRA13 was grown in HeLa S3 suspension cells (Alexander WA et.al., 1992). RNAi was performed as previously described(Sabin LR et.al., 2009). Cells were infected for 4 days as follows: DCV MOI=7; RVFV MOI=17; VACV MOI=383; VSV MOI=4.

extract_protocol: 40 mg of total RNA was separated on a 15% TBE-urea gel and smRNAs ~15-29 nt were excised and eluted. Following ethanol precipitation, smRNA-seq libraries were produced using the Small RNA Sample Prep v1.5 kit (Illumina, San Diego, CA) as per manufacturer's instructions.

treatment_protocol: dl1 cells are infected by 4 different viruses (DCV, RVFV, VACV and VSV)

tag: virus-treatment

value: VSV

value: Ago2 knockdown


title: VSV_Drosha

description:
vsiRNA from VSV-infected Drosha knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VSV-infected Drosha knockdown dl1 cells

value: Drosha knockdown


title: VSV_Dcr2

description:
vsiRNA from VSV-infected Dcr2 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VSV-infected Dcr2 knockdown dl1 cells

value: Dcr2 knockdown


title: LS1034_2


title: VSV_Dcr1

description:
vsiRNA from VSV-infected Dcr1 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VSV-infected Dcr1 knockdown dl1 cells

value: Dcr1 knockdown


title: VACV_Dcr1

description:
vsiRNA from VACV-infected Dcr1 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VACV-infected Dcr1 knockdown dl1 cells

value: VACV


title: VACV_Dcr2

description:
vsiRNA from VACV-infected Dcr2 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VACV-infected Dcr2 knockdown dl1 cells


title: VACV_Drosha

description:
vsiRNA from VACV-infected Drosha knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters


title: VSV_BGAL

description:
vsiRNA from VSV-infected control dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VSV-infected control dl1 cells

value: control


title: VSV_Ago1

description:
vsiRNA from VSV-infected Ago1 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VSV-infected Ago1 knockdown dl1 cells

value: Ago1 knockdown


title: VACV_Ago2

description:
vsiRNA from VACV-infected Ago2 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VACV-infected Ago2 knockdown dl1 cells


title: VACV_GFP

description:
vsiRNA from VACV-infected control dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VACV-infected control dl1 cells


title: RVFV_Drosha

description:
vsiRNA from RVFV-infected Drosha knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

value: RVFV


title: RVFV_Dcr2

description:
vsiRNA from RVFV-infected Dcr2 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: RVFV-infected Dcr2 knockdown dl1 cells


title: RVFV_Dcr1

description:
vsiRNA from RVFV-infected Dcr1 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: RVFV-infected Dcr1 knockdown dl1 cells


title: VACV_Ago1

description:
vsiRNA from VACV-infected Ago1 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: VACV-infected Ago1 knockdown dl1 cells


title: DGM-11133_sm

status: Public on Aug 05 2013

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: gene expression

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: small airway epithelium (SAE), S

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: S


title: RVFV_Ago1

description:
vsiRNA from RVFV-infected Ago1 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: RVFV-infected Ago1 knockdown dl1 cells


title: DGM-11103_sm

description: gene expression


title: RVFV_BGAL

description:
vsiRNA from RVFV-infected control dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: RVFV-infected control dl1 cells


title: DCV_Dcr1

description:
vsiRNA from DCV-infected Dcr1 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: DCV-infected Dcr1 knockdown dl1 cells

value: DCV


title: DCV_Drosha

description:
vsiRNA from DCV-infected Drosha knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: DCV-infected Drosha knockdown dl1 cells


title: DCV_Dcr2

description:
vsiRNA from DCV-infected Dcr2 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: DCV-infected Dcr2 knockdown dl1 cells


title: DCV_Ago1

description:
vsiRNA from DCV-infected Ago1 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: DCV-infected Ago1 knockdown dl1 cells


title: DCV_Ago2

description:
vsiRNA from DCV-infected Ago2 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: DCV-infected Ago2 knockdown dl1 cells


title: Malish7_XTC_rep1

status: Public on Mar 02 2013

city: Marseille

first: Aurélie

last: Renvoisé

address: 27 bd Jean Moulin

country: France

institute: Urmite

data_processing: Illumina Genome Analyzer Pipeline (goat), Firecrest version 1.4.0 software was used to qualify reads passing default signal quality filters. Raw data were trimmed for adaptaters’ removal; reads were cleaned for removing and trimming polyA/Ts and undetermined bases (N) using in house Perl scripts (GATC Biotech, Konstanz, Germany). Clustering was performed using Cd-hit, a clustering algorithm using 100% sequence similarity 30. We mapped clustered data on the genome of R. conorii strain Malish 7 (CLC Genomics). We selected sequences with coverage superior to 100X (which represents more than 10 times the average global coverage) and we extracted clustered “candidate sequences”.

organism: Rickettsia conorii str. Malish 7

source_name: Reference strain

growth_protocol: R. conorii subsp. conorii strain Malish 7 was cultivated on XTC cells for 3 days at 28°C.

extract_protocol: Samples were diluted in 200 µl TE pH 7.8, and then incubated for 10 min at room temperature in the presence of lysozyme (10 mg/ml). Obtained supernatants were treated following miRNeasy purification kit protocol (Qiagen). Enriched fractions of small RNAs (<200 nt) were obtained. RNA samples were treated by TURBO DNA Free kit (Ambion) and the absence of residual DNA was systematically confirmed by real time PCR. Final RNA was characterized using small RNA chips (Agilent) combined with Bioanalyzer Agilent 2100. Enriched fraction of small RNA was separated on a denaturing 15% polyacrylamide gel. Small RNA fraction with a length of 19-29 bases was obtained by passive elution of the RNA from the gel. The eluted RNA was precipitated with ethanol and dissolved in water. Obtained miRNA were poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adapter to the 5´-phosphate of the miRNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase. The primers used for PCR amplification were designed for amplicon sequencing according to the instructions of Illumina/Solexa. Illumina Genome Analyzer libraries were analyzed following the manufacturer’s instructions; 36 cycles of sequencing-by-synthesis were performed, the library ran in one lane of a flowcell using the Genome Analyzer.

treatment_protocol: Infected cells were collected and treated in the presence of 1% trypsin in K36 buffer for 1h at 37°C, then centrifuged and digested by DNase I for 1h at 37°C to reduce eukaryotic DNA contamination, as previously reported 28. Samples were loaded on one renograffin gradient (26-38-45) to isolate bacteria from residual eukaryotic residues. The band of purified bacteria was washed in K36 buffer and treated again by DNase I. The sample was resuspended in PBS buffer, aliquoted, and stored at -80°C.

tag: cell type

value: XTC

tag: growth temperature

tag: growth duration

value: 3 days

tag: strain

value: Malish 7


title: Chlamydomonas reinhardtii 2137 - NH4Cl supplementation experiment - [NH4Cl]=7mM

status: Public on Jan 10 2013

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description: Illumina's RNA-Seq whole transcriptome analysis

library_source: non-genomic

data_processing:
RNAs were sequenced at Illumina and Los Alamos National Laboratory on a GAIIx system for estimating transcript abundance in each of the three N-deficiency time course experiments. The reads were aligned using bowtie  in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Processed files correpond to the bowtie standard output format.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Chlamydomonas reinhardtii strains CC-3269/ 2137 (wild-type nit2 mt+) were cultured at 24°C (180 rpm, ~90 mmol/m2/s, cool white fluorescent bulbs at 4100K and warm white fluorescent bulbs at 3000K were used in the ratio of 2:1) in TAP medium, -N TAP or TAP suppemented with various amounts of NH4

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced  by whole transcriptome analysis.

treatment_protocol: N-starved cells were grown to approximately 4x10^6 cells/mL, collected by centrifugation (2170 xg, room temperature, 5 min), washed and resuspended in the same medium to 2 x 10^6 cells/mL. For growth in reduced nitrogen, N-free TAP medium supplemented with NH4Cl to 7, 3.5, 1.75, 0.7 or 0.35 mM. Cultures were inoculated to 1x10^5 cells/mL and collected for RNA at 1 x 10^6 cells/mL, when the growth rates of all cultures were identical

tag: treatment

tag: medium

value: TAP

tag: sequencing cycles / read length

tag: library type

value: single-end


title: DCV_BGAL

description:
vsiRNA from DCV-infected control dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: DCV-infected control dl1 cells

tag: cell line


title: Chlamydomonas reinhardtii 2137 - NH4Cl supplementation experiment - [NH4Cl]=3mM


title: Chlamydomonas reinhardtii 2137 - NH4Cl supplementation experiment - [NH4Cl]=1.75mM


title: Chlamydomonas reinhardtii 2137 - NH4Cl supplementation experiment - [NH4Cl]=0.7mM


title: WP3ΔSW1-4°C, rep2

status: Public on Jan 30 2013

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

description:
WP3ΔSW1-4℃-rep2
WP3ΔSW1 cDNA was labeled with Cy3, and WP3 wild-type cDNA was labeled with Cy5.

hyb_protocol: Samples were hybridized to Shewanella piezotolerans WP3 whole genome microarrays.

scan_protocol: All microarrays were scanned with a LuxScan 10K scanner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensities of individual spots from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing: S-Plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data were log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model. Microarray spots with P values <0.001 in the F-test and log2 ratio were regarded as differentially expressed genes. In addition, all of the DEGs were confirmed with Significance Analysis of Microarrays (SAM) software.

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol:
The retro-transcription of the 20 μg total RNA was according to the Invitrogen manufacturer's instructions. cDNA labeled with a fluorescent dye (Cy5- and Cy3-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction.
Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt II (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl) shaking at 220 rpm at 4°C.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

tag: strain/background

tag: genotype/variation

value: wild-type

tag: culture conditions

value: 4℃ in 2216E medium

source_name: WP3ΔSW1 cells at mid-exponential phase


title: RVFV_Ago2

description:
vsiRNA from RVFV-infected Ago2 knockdown dl1 cells
*loc.txt : alignment files for NR-seq on corresponding virus genomes
*info.txt : NR-seq clone-number and length information after trimming of 3'-adapters
*seq.fasta : fasta sequence file for NR-seq after trimming of 3'-adapters

source_name: RVFV-infected Ago2 knockdown dl1 cells

value: Ago2 knockdown


title: Chlamydomonas reinhardtii 2137 - NH4Cl supplementation experiment - [NH4Cl]=0.35mM


title: WP3ΔSW1-4°C, rep1

description:
WP3ΔSW1-4℃-rep1
WP3ΔSW1 cDNA was labeled with Cy5, and WP3 wild-type cDNA was labeled with Cy3.


title: H9 PluriSIn #1 (2)

status: Public on Jan 22 2013

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

description: Gene expression data from undifferentiated pluripotent stem cells grown on matrigel with mTeSR1 and exposed to PluriSIn #1 at 20uM with 0.02% DMSO for 12 h.

hyb_protocol: Affymetrix protocol, 11ug cRNA.

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4.

data_processing: Affymetrix Expression Console MAS5.

source_name: H9, PluriSIn #1

label_protocol: 200ng total RNA, Affymetrix protocol.

growth_protocol: Cells were grown on matrigel-coated plates using mTeSR1 defined medium.

extract_protocol: Total RNA was isolated using 5 Prime RNA isolation kit.

treatment_protocol: Undifferentiated pluripotent stem cells were grown on matrigel with mTeSR1 and exposed to PluriSIn #1 at 20uM with 0.02% DMSO for 12 h.

value: undifferentiated human embryonic stem cells

tag: age

value: passage 52

value: PluriSIn #1


title: CSES2-SO2/3 early endodermal progenitors PluriSIn #1

description: Gene expression data from 8d-differentiated early endodermal progenitor cells exposed to PluriSIn #1 at 20uM 0.02% DMSO for 12 h.

source_name: CSES2-SO2/3 early endodermal progenitors, PluriSIn #1

growth_protocol: Cells were grown according to the protocol of Duan et al. (Stem Cells, 2010)

treatment_protocol: 8d-differentiated early endodermal progenitor cells were exposed to PluriSIn #1 at 20uM 0.02% DMSO for 12 h.

value: human embryonic stem cells differentiated into early endodermal progenitor cells

value: passage 35


title: H9 PluriSIn #6

description: Gene expression data from undifferentiated pluripotent stem cells grown on matrigel with mTeSR1 and exposed to PluriSIn #6 at 20uM with 0.02% DMSO for 12 h.

source_name: H9, PluriSIn #6

treatment_protocol: Undifferentiated pluripotent stem cells were grown on matrigel with mTeSR1 and exposed to PluriSIn #6 at 20uM with 0.02% DMSO for 12 h.

value: PluriSIn #6


title: NSCLC 5

status: Public on Sep 16 2012

city: Zhoushan

first: lina

last: ma

address: Renmin North Road No.238

institute: Zhoushan Hospital

description:
SAMPLE 9
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalisation with Illumina Genomestudio software

source_name: lung

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with 1% agrose electrophoresis   .

tag: gender

value: male

tag: disease state

value: NSCLC

tag: nsclc type

value: adenocarcinoma

tag: tissue

value: cancer

tag: tnm


title: NSCLC 2

description:
SAMPLE 3
replicate 1

value: squamous


title: adjacent normal tissue 5

description:
SAMPLE 10
replicate 1

value: adjacent normal


title: adjacent normal tissue 4

description:
SAMPLE 8
replicate 1


title: NSCLC 6

description:
SAMPLE 11
replicate 1


title: NSCLC 3

description:
SAMPLE 5
replicate 1


title: NSCLC 4

description:
SAMPLE 7
replicate 1


title: Small RNAs from young mouse brain (5 months)

status: Public on Jun 01 2012

city: NEW HAVEN

first: ALEXANDRE

last: DE LENCASTRE

address: 219 PROSPECT ST KBT 924

institute: YALE UNIVERSITY

data_processing:
s_1_sop_rr.tab; genome build: mm9, NCBI Build 37
The software program Soap was used to align raw sequences to the reference mouse genome, mm9, NCBI Build 37, (obtained from http://genome.ucsc.edu) and sequences corresponding to the 3'-end cloning adapter TCGTATGCCGTCTTCTGCTTGT were removed, allowing a maximum of 3 mismatches in the adapter (option -S 3 in Soap). The resulting total number of genome-aligned reads was 11,181,999 (80%). The number of sequence reads that correspond to known miRNAs - 7,049,494 (63% of genome-matching reads) - was determined by perfect sequence matching to the database of known miRNAs (miRBase release 16).

organism: Mus musculus

source_name: Brain

extract_protocol: RNA from mouse brains was extracted as previously described (Ausubel et al., Current Protocols in Molecular Biology, 1987). In short, frozen tissues were homogenized, and lysates were thawed and phenol extracted. Resulting RNA pellets were dissolved in Nuclease Free water (Ambion, Austin, TX, USA), and stored at -80˚C. Small RNAs from young and old mouse brains were purified and prepared for Illumina sequencing, according to the manufacturer’s recommendations. 10μg of total RNA extracted from each of four mouse brains (two old and two young) were electrophoresed through a 15% TBE-urea PAGE gel. The fraction of the lanes containing RNA molecules between 18–30 nucleotides in length was excised from the gel. RNA was isolated from the gel slices and ethanol precipitated. Isolated small RNAs were then fitted with 5ʹ and 3ʹ adapters, and reverse transcribed, all in accordance with the manufacturer’s protocol. Resulting cDNA was PCR amplified using Illumina primers, and PCR amplicons were electrophoresed, excised from polyacrylamide gels and ethanol precipitated. Purified DNA libraries from the olds brains were combined, as were purified DNA libraries from the young brains. Each cDNA library (old mix and young mix) was subsequently sequenced by Illumina sequencing technology.

tag: developmental stage

value: Adult

value: Brain

value: 5 months

tag: Sex

value: Male


title: adjacent normal tissue 6

description:
SAMPLE 12
replicate 1


title: H9 control (1)

description: Gene expression data from undifferentiated pluripotent stem cells grown on matrigel with mTeSR1 and exposed to 0.02% DMSO for 12 h.

source_name: H9, control

treatment_protocol: Undifferentiated pluripotent stem cells were grown on matrigel with mTeSR1 and exposed to 0.02% DMSO for 12 h.

tag: cell type

value: DMSO vehicle


title: Small RNAs from aged mouse brain (24-25 months)

data_processing:
s_2_sop_rr.tab; genome build: mm9, NCBI Build 37
The software program Soap was used to align raw sequences to the reference mouse genome, mm9, NCBI Build 37, (obtained from http://genome.ucsc.edu) and sequences corresponding to the 3'-end cloning adapter TCGTATGCCGTCTTCTGCTTGT were removed, allowing a maximum of 3 mismatches in the adapter (option -S 3 in Soap). The resulting total number of genome-aligned reads was 11,181,999 (80%). The number of sequence reads that correspond to known miRNAs - 7,049,494 (63% of genome-matching reads) - was determined by perfect sequence matching to the database of known miRNAs (miRBase release 16).

value: 24-25 months

tag: strain


title: adjacent normal tissue 1

description:
SAMPLE 2
replicate 1


title: NSCLC 1

description:
SAMPLE 1
replicate 1


title: adjacent normal tissue 3

description:
SAMPLE 6
replicate 1


title: H9 PluriSIn #1 (1)

value: undifferentiated human embryonic stem cells

value: passage 52

tag: treatment


title: H9 control (2)


title: CSES2-SO2/3 early endodermal progenitors control

description: Gene expression data from 8d-differentiated early endodermal progenitor cells exposed to 0.02% DMSO for 12 h.

source_name: CSES2-SO2/3 early endodermal progenitors, control

treatment_protocol: 8d-differentiated early endodermal progenitor cells were exposed to 0.02% DMSO for 12 h.

value: human embryonic stem cells differentiated into early endodermal progenitor cells


title: adjacent normal tissue 2

description:
SAMPLE 4
replicate 1


title: CTR_mmg_I (PBL of healthy donor I, mmg condition)

status: Public on Apr 09 2012

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 5% sensitivity settings.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 60% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were and inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.

source_name: PBL of healthy donor I in modelled microgravity (control-mmg).

label_protocol: We performed miRNA expression profiling from 200 ng of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies). Total RNA was dephosphorylated and ligated with pCp-Cy3. Unincorporated dyes were removed with MicroBioSpin6 columns (BioRad) . Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes.

extract_protocol: Total RNA was isolated from 107 cells by using Trizol® Reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 20% were used for microarray analysis.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named I, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

tag: individual

value: donor I

value: modeled microgravity (MMG) condition

tag: sample name

value: CTR-mmg-I


title: PBMC_206_day70

description:
206_day70
Gene expression data from PBMC extracted from individual 206 70 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 206 at day70

tag: individual id

value: peripheral blood mononuclear cells (PBMC)

value: male

tag: ethnicty

value: Asain

tag: sample collection time

value: 70 days post vaccination (day70)


title: CTR_mmg_L (PBL of healthy donor L, mmg condition)

source_name: PBL of healthy donor L in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named L, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: donor L

value: CTR-mmg-L


title: CTR_1g_L (PBL of healthy donor L, 1g condition)

source_name: PBL of healthy donor L in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named L, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: 1g condition


title: CTR_1g_F (PBL of healthy donor F, 1g condition)

source_name: PBL of healthy donor F in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named F, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: donor F


title: CTR_1g_I (PBL of healthy donor I, 1g condition)

source_name: PBL of healthy donor I in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named I, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).


title: CTR_mmg_H (PBL of healthy donor H, mmg condition)

status: Public on Apr 10 2012

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed with Agilent Gene Expression wash buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 90% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were inter-array normalized with Quantile normalization (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed. Principal component analysis, cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. Methods in Enzymology. 2006;411:134-93). Identification of differentially expressed genes was performed with one and two class Significance Analysis of Microarray (SAM) program (Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci USA 2001;98:5116-121) with default settings. SAM uses a permutation-based multiple testing algorithm and identifies significant genes with variable false-discovery rates (FDR). This can be manually adjusted to include a reasonable number of candidate genes with acceptable and well defined error probabilities.

source_name: PBL of healthy donor H in modelled microgravity (control-mmg).

label_protocol: Eight hundred nanograms of total RNA were labelled with “Agilent One-Color Microarray-Based Gene Expression protocol” (Agilent) according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labelled with cyanine 3-labelled nucleotide. Labelled cRNA was purified with RNeasy Mini columns (Qiagen). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurement (NanoDrop Technologies).

extract_protocol: Total RNA was isolated from 107 cells by using Trizol® Reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, were used for microarray analysis.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named H, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: donor H

value: CTR-mmg-H


title: CTR_1g_G (PBL of healthy donor G, 1g condition)

source_name: PBL of healthy donor G in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named G, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: donor G


title: CTR_1g_H (PBL of healthy donor H, 1g condition)

source_name: PBL of healthy donor H in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named H, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).


title: CTR_mmg_F (PBL of healthy donor F, mmg condition)

source_name: PBL of healthy donor F in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named F, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: CTR-mmg-F


title: CTR_mmg_C (PBL of healthy donor C, mmg condition)

source_name: PBL of healthy donor C in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named C, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: donor C

value: CTR-mmg-C


title: CTR_mmg_G (PBL of healthy donor G, mmg condition)

source_name: PBL of healthy donor G in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named G, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: CTR-mmg-G


value: modeled microgravity (MMG) condition

value: Human Peripheral blood lymphocytes (PBL)


title: PBMC_206_day1

description:
206_day1
Gene expression data from PBMC extracted from individual 206 1 day post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 206 at day1

treatment_protocol: Individuals were vaccinated with the 2009 Fluvirin seasonal influenza (Novartis), and H1N1 pandemic (Sanofi-Aventis) vaccines, both without adjuvant.

value: peripheral blood mononuclear cells (PBMC)

value: 1 day post vaccination (day1)


title: CTR_1g_E (PBL of healthy donor E, 1g condition)

source_name: PBL of healthy donor E in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named E, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: donor E


title: CTR_mmg_D (PBL of healthy donor D, mmg condition)

source_name: PBL of healthy donor D in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named D, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: donor D

value: CTR-mmg-D


title: CTR_mmg_E (PBL of healthy donor E, mmg condition)

source_name: PBL of healthy donor E in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named E, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: CTR-mmg-E


title: CTR_1g_D (PBL of healthy donor D, 1g condition)

source_name: PBL of healthy donor D in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named D, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: 1g condition


title: CTR_1g_A (PBL of healthy donor A, 1g condition)

source_name: PBL of healthy donor A in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named A, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: donor A


title: CTR_1g_M (PBL of healthy donor M, 1g condition)

source_name: PBL of healthy donor M in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named M, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: donor M


title: CTR_mmg_M (PBL of healthy donor M, mmg condition)

source_name: PBL of healthy donor M in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named M, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: CTR-mmg-M


title: CTR_mmg_P (PBL of healthy donor P, mmg condition)

source_name: PBL of healthy donor P in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named P, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: donor P

value: CTR-mmg-P


title: CTR_1g_C (PBL of healthy donor C, 1g condition)

source_name: PBL of healthy donor C in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named C, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: donor C


title: CTR_1g_P (PBL of healthy donor P, 1g condition)

source_name: PBL of healthy donor P in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named P, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).


value: donor G


title: CTR_mmg_A (PBL of healthy donor A, mmg condition)

source_name: PBL of healthy donor A in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named A, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: CTR-mmg-A


value: modeled microgravity (MMG) condition

value: CTR-mmg-C


value: Human Peripheral blood lymphocytes (PBL)


title: FLAG-AGO1-CMV∆2b_IP_rep1_At_matches

status: Public on Mar 01 2012

city: Riverside

first: JUAN

last: JOVEL

state: CA

address: 3401 Watkins Drive

department: Plant Pathology

institute: University of California Riverside

data_processing:
Reads were extracted using the Illumina pipeline.  Trimming of adapters and down-stream analyses were carried out with in-house Perl scripts, except alignments of short reads to Arabidopsis or CMV sequences, which were performed with bowtie (no mistmatches were allowed).
All sequences containing perfect match 5' barcode (ATC/CGT/TAC) and at least 6 sucessive perfect-matched nucleotides of the 3' linker were kept for later analysis. The barcode and linker sequences were computationally removed by in-house perl scripts. All trimmed sequences in length of 18-30nt were aligned with CMV genome and the perfect matched reads were used for all further analysis.

source_name: Systemically-infected leaves

growth_protocol: Arabidopsis plants were grown in our glass houses under stardard conditions.

extract_protocol:
Low molecular weight RNAs extracted by Trizol (Invitrogen) from the systemically infected leaves 14 days after inoculation with CMV-Δ2b were purified from 15% denatured polyacrylamide gel. Purified small RNAs were directly ligated to the 3′-linkers for miRNA cloning (Integrated DNA Technology) by T4 RNA ligase 2Tr (New England Biolabs). The ligation products were purified and ligated to a suitable 5′ Solexa linker by T4 RNA ligase I (New England Biolabs). The final ligation products were reverse transcribed using a primer targeting the 3′-linker and the cDNA pool was amplified by PCR and sequenced by the Solexa technology (Illumina) in our campus facility. Duplicate libraries were constructed from two independent RNA samples.
immunoprecipitation: Three g systemic leaves from FLAG-AGO1 or HA-AGO2 plants infected with CMV-Δ2b were ground to powder in liquid nitrogen and supplied with 10 ml of extraction buffer [20 mM Tris•HCl, pH 7.5/300 mM NaCl/5 mM MgCl2/5 mM DTT/1% plant protease inhibitor mixture (Sigma)].  The suspension was clarified by centrifugation (10 min, 4ºC, 14,000 rpm) and the supernatant filtered through cheesecloth. The filtered supernatant was incubated with anti-FLAG M2 agarose (Sigma-Aldrich) or anti-HA affinity matrix (Roche), according to manufacturers’ protocols, for 4h at 4ºC.  The beads were then washed twice with extraction buffer supplemented with 0.5% Nonidet P-40 and the AGO-bound RNA extracted with TRIzol.

tag: genotype

tag: genotype reference

value: Baumberger & Baulcombe 2005. PNAS 102(33):11928-33.

tag: source

value: FLAG immunoprecipitation

tag: antibody

value: anti-FLAG M2

tag: vendor

value: Sigma-Aldrich


title: FLAG-AGO1-CMV∆2b_IP_rep2_CMV_matches


title: FLAG-AGO1-CMV∆2b_IP_rep1_CMV_matches


title: HA-AGO2-CMV∆2b_IP_rep1_CMV_matches

value: HA immunoprecipitation

value: anti-HA

value: Roche


title: HA-AGO2-CMV∆2b_IP_rep1_At_matches


title: loqs_FHVdB2_matches

status: Public on Nov 12 2011

data_processing: Reads were extracted using the Illumina pipeline.  Trimming of adapters and down-stream analyses were carried out with in-house Perl scripts, except alignments of short reads to FHV or endogenous sequences, which were performed with bowtie (no mistmatches were allowed).

source_name: Adult flies intrathoracically-injected with FHVdeltaB2

growth_protocol: Flies were reared on standard cornmeal-agar medium at room temperature.

extract_protocol: Total RNA was extracted by Trizol (Invitrogen) from whole flies at 7 days after inoculation with FHV-deltab2 or FHV and 18-28-nt small RNAs were purified from 15% denatured polyacrylamide gel. Purified small RNAs were directly ligated to the 3'-linkers for miRNA cloning (Integrated DNA Technology) by T4 RNA ligase 2Tr (New England Biolabs). The ligation products were purified and ligated to a suitable 5' Solexa linker by T4 RNA ligase I (New England Biolabs). The final ligation products were reverse transcribed using a primer targeting the 3'-linker and the cDNA pool was amplified by PCR and sequenced by the Solexa technology (Illumina) in our campus facility.

value: loqs[f00791], loqs[KO-]

value: Forstermann et al., 2005. PLoS Biol 3:e236; Marques et al., 2010. Nat Struct Mol Biol 17:24-30; Park et al., 2007 Curr Biol 17:533-538.


title: CR_muscle_RNA-Seq

status: Public on Nov 22 2011

city: Elk Grove

first: joseph

middle: M

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

description: 76-bp paired-end mRNA-Seq

data_processing: Paired end sequencing reads were aligned to the mouse reference genome (NCBI37/mm9) with Tophat v1.2.0 and further processed by Cufflinks to assemble transcripts and to measure their relative abundances in FPKM units. Assembled transcripts were tested for differential expression between control and CR using the Cuffcompare and Cuffdiff utilities included in the Cufflinks package. Differential splicing and promoter usage were also assessed, and novel isoforms of annotated genes were reported.

molecule: polyA RNA

source_name: thigh muscles

extract_protocol: Poly(A)+ mRNA was purified from 10 µg of total RNA, and fragmented (~200nt) prior to cDNA synthesis with random priming. The cDNA was converted into paired-end libraries using the Illumina mRNA-Seq Sample Prep Kit according to the manufacturer’s protocol.

treatment_protocol: The CR mice consumed ∼40% fewer calories than the control group for 25 months. The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram of body weight as the control mice.

tag: age

value: 26 months

tag: tissue

value: skeletal muscle

tag: stress

value: calorie restriction


title: ago2_FHVdB2_matches


title: FLAG-AGO1-CMV∆2b_IP_rep2_At_matches


title: dcr2_FHVdB2_matches


title: Control_muscle_RNA-Seq

description: 76-bp paired-end mRNA-Seq

value: control


title: wt_FHV_matches

source_name: Adult flies intrathoracically-injected with FHV

value: Canton S (csw)


title: wt_FHVdB2_matches


value: donor A

value: modeled microgravity (MMG) condition

value: CTR-mmg-A


value: 1g condition

value: Human Peripheral blood lymphocytes (PBL)


value: donor P

value: CTR-mmg-P


title: HA-AGO2-CMV∆2b_IP_rep2_CMV_matches

value: HA immunoprecipitation


title: miRNA_LA_4

status: Public on Sep 10 2011

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

description: small RNA seq of Left atrial tissue

data_processing:
Basecalls performed using CASAVA version 1.3
For the poly-A enriched mRNA samples, reads were aligned to hg19 using tophat with the following parameters -r 0 --solexa1.3-quals -G hg19gene.gtf
For the miRNA-seq data, reads were aligned to miRBase Release 17 hairpins using bowtie with the -best option and allowing for 1 mismatch.  Aligned reads were then collapsed down to mature sequences.
genome build: hg19
processed data files format and content: Counts were obtained from the BAM files using custom scripts.

source_name: Left Atrial Tissue

extract_protocol: Total RNA was extracted using QIAGEN miRNeasy Mini Kits from 20 mg of atrial tissue samples.  Sequencing libraries were made following Illumina's mRNA protocol.  Briefly, RNA was purified by poly-A selection using oligo(dT) beads and chemically fragmented.  First and second strand cDNA synthesis was followed by end-repair and 3' adenylation.  5' and 3' Illumina adapters were ligated and size-selected using gel-purification and PCR amplification.   Using the same total RNA preparations, a smallRNA-sequencing library was constructed following Illumina's Alternative v1.5 smallRNA-seq protocol (Part # 15002615).  Briefly, 5' and 3' adapters were ligated onto the small RNAs and amplified.  The cDNA with adapters was size selected between 93-100 bp and 36 bp single-end sequencing was performed.

value: Left Atrial Heart


title: HA-AGO2-CMV∆2b_IP_rep2_At_matches

value: anti-HA

value: Roche


title: miRNA_RA_3

description: small RNA seq of Right atrial tissue

source_name: Right Atrial Tissue

value: Right Atrial Heart


title: miRNA_LA_3

description: small RNA seq of Left atrial tissue


title: miRNA_LA_2

description: small RNA seq of Left atrial tissue


title: miRNA_LA_1

description: small RNA seq of Left atrial tissue


title: miRNA_RA_2

description: small RNA seq of Right atrial tissue


title: miRNA_RA_1

description: small RNA seq of Right atrial tissue


title: JMM-cel-012_fem-1_AD_5'INDEP-1

status: Public on Jun 01 2011

city: Stanford

first: Jay

last: Maniar

address: 300 Pasteur Dr L302

institute: Stanford University

description: barcode: TATG

data_processing: Raw data only (no processing performed).

organism: Caenorhabditis elegans

source_name: Adult hermaphrodite

extract_protocol: Small RNAs were size-selected (Ambion - miRvana).  We then captured the 3' end (IDT-Linker-1 or IDT-Linker-2).  These 3'-captured small RNAs were then further size selected and treated first with antarctic phosphatase and T4 polynucleotide kinase.  Subsequently, these treated RNAs were ligated to a barcoded 5' adapter, reverse transcribed, amplified and sequenced.

tag: rna-seq method


title: JMM-cel-009_ego-1_fem-1_AD_5'INDEP-1

description: barcode: GTTA


title: miRNA_RA_4

description: small RNA seq of Right atrial tissue


title: r2d2 / r2d2

status: Public on Feb 10 2011

city: Munich

first: Klaus

last: Förstemann

address: Feodor-Lynen 25

department: Gene Center

institute: Ludwig-Maximilians University

data_processing: Perl scripts were used to sort according to barcodes, remove the 3'-linker sequences and select for 19-25 nt long inserts (available upon request). Bowtie was used for mapping against the target sequences specified in the manuscript.

source_name: head & thorax

growth_protocol: standard fly medium

extract_protocol: RNA was size-fractionated by polyacrylamide/urea gel electrophoresis and 19-25 nt long small RNAs were excised. This was followed by ligation of a pre-adenylated linker (AMP-5’p=5’pCTGTAGGCACCATCAATdideoxyC-3’) to the 3'-end, gel-purification of the ligation product and subsequent ligation of a 5'-adapter (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3' ). Reverse transcription was primed with oligo 5’-ATTGATGGTGCCTACAG-3’, then barcodes and Illumina linkers were added with oligos 5'-AATGATACGGCGACCACCGAACACTCTTTCCCT ACACGACG-3' (5'-end, no barcode) and 5'-CAAGCAGAAGACGGCATACGGATCCGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACCAGCTGGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACTCTAGAGATTGATGGTGCCTACAG-3' or 5'-CAAGCAGAAGACGGCATACATCGATGATTGATGGTGCCTACAG-3' (3'-end, barcode-sontaining primers).

treatment_protocol: dissection of head & thorax to separate somatic and germ line parts

tag: genotype/variation

tag: developmental stage

value: adult


title: r2d2 / Cyo


title: loqs ko / loqs ko

value: loqs ko/loqs ko


title: loqs-ko / CyO

value: loqs-ko/CyO


title: SVir-8d

status: Public on Nov 01 2011

city: Montpellier

first: piquemal

last: david

address: 134 rue du Curat

institute: Skuld Tech

description:
anchor: NlaIII
tag_length: 17
tag_count: 3621470

data_processing: The sequence files of each DGE library were analyzed with BIOTAG software (Skuldtech, Montpellier, France) (Piquemal et al. Genomics 2002) for tag detection, tag counting and for assessing DGE library quality.

organism: Magallana gigas

source_name: Infected oyster hemocytes

extract_protocol: TRIzol protocol

treatment_protocol: The DGE library SVir-8d was constructed from Crassostrea gigas oyster hemocytes collected 8 days before an experimental infection by virulent Vibrio species (V. splendidus LGP32 and V. aestuarianus LPi 02/41 Type I). Only animals that survived infection were used.

value: 12 months

tag: gender

value: mixed

tag: cell type

value: hemocytes

tag: treatment

value: virulent Vibrio infection (V. splendidus LGP32 and V. aestuarianus LPi 02/41 Type I)


title: SaVir

description:
anchor: NlaIII
tag_length: 17
tag_count: 3652097

treatment_protocol: The DGE library SaVir was constructed from hemocytes collected, 4 days after challenge, from Crassostrea gigas oysters that survived an experimental infection by avirulent Vibrio tasmaniensis LMG 20012T.

value: avirulent Vibrio infection (V. tasmaniensis LMG 20012T)


title: SVir

description:
anchor: NlaIII
tag_length: 7
tag_count: 3367152

treatment_protocol: The DGE library SVir was constructed from hemocytes collected, 4 days after challenge, from Crassostrea gigas oysters that survived an experimental infection by a virulent Vibrio species (V. splendidus LGP32 and V. aestuarianus LPi 02/41 Type I).


title: Patient ID_241

status: Public on Dec 30 2010

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

country: Japan

institute: Tokyo Medical University

hyb_protocol: labeled RNA was hybridized to Agilent miRNA array ( 8 arrays per slide) at 55°C for 20h in rotisserie in a hybridization oven. Disassembled arrays was washed in GE wash buffer 1&2 for 5 minutes each.

scan_protocol: Images was scanned with Agilent scanner at 5µm resolution

data_processing: The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed.

source_name: Liver, ID_241

label_protocol: 100ng total RNA was dephosphorylated at the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was then ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.0

extract_protocol: Total RNA was extracted by using mirVana™ miRNA Isolation Kit (Ambion) according to manufacturer’s instruction

value: liver (chronic hepatitis)

tag: drug-response

value: sustained virological responder

tag: age (years)

tag: sex

value: Male

tag: type of hcv

tag: degree of inflammation/fibrosis


title: Patient ID_238

source_name: Liver, ID_238


title: Patient ID_239

source_name: Liver, ID_239

value: transient virological responder


title: Patient ID_242

source_name: Liver, ID_242

value: non-virological responder

value: Female


title: Patient ID_240

source_name: Liver, ID_240


title: Patient ID_243

source_name: Liver, ID_243


title: Patient ID_244

source_name: Liver, ID_244


title: NSVir-8d

description:
anchor: NlaIII
tag_length: 17
tag_count: 3866796

treatment_protocol: The DGE library NSVir-8d was constructed from Crassostrea gigas oyster hemocytes collected 8 days before an experimental infection by virulent Vibrio species (V. splendidus LGP32 and V. aestuarianus LPi 02/41 Type I). Only animals that did not survive infection were used.


title: Patient ID_237

source_name: Liver, ID_237


title: Patient ID_234

source_name: Liver, ID_234


title: Patient ID_236

source_name: Liver, ID_236


title: Patient ID_232

source_name: Liver, ID_232


title: Patient ID_231

source_name: Liver, ID_231


title: Patient ID_228

source_name: Liver, ID_228


title: Patient ID_222

source_name: Liver, ID_222


title: Patient ID_223

source_name: Liver, ID_223


title: Patient ID_220

source_name: Liver, ID_220


title: Patient ID_230

source_name: Liver, ID_230


title: Patient ID_229

source_name: Liver, ID_229


title: Patient ID_221

source_name: Liver, ID_221


title: Patient ID_219

source_name: Liver, ID_219


title: Patient ID_216

source_name: Liver, ID_216


title: Patient ID_215

source_name: Liver, ID_215


title: Patient ID_217

source_name: Liver, ID_217


title: Patient ID_213

source_name: Liver, ID_213


title: Patient ID_214

source_name: Liver, ID_214


title: -N+3h

status: Public on Apr 21 2011

city: Esch-Belval

first: Patrick

last: May

state: Luxembourg

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

description: small RNA

data_processing: Removed adaptores. Sequences without adapters and low complexity sequences were discarded.

source_name: Arabidopsis thaliana wild-type seedlings

growth_protocol: Nine-day old nutrient-replete and N- and P-limited wild-type Arabidopsis thaliana Col-0 seedlings were grown in sterile liquid cultures as described previously (Scheible et al, Plant Physiol. 2004; Morcuende et al, Plant Cell & Environ. 2007)

extract_protocol: see Pant et al, Plant Physiol. 2009

tag: ecotype

value: Columbia (Col-0)

value: Nitrogen limiting for 3 hours


title: Japonica DGE analysis

status: Public on Nov 04 2011

city: Kunming

first: xin

last: li

address: 32 Jiaochang Road

institute: Kunming Insititute of Zoology, Chinese Academy of Sciences,P.R.China

description:
DGE analysis.
anchor: NlaIII
tag length: 21
tag count: 612176

data_processing: Full-length cDNA sequences of rice representative gene were downloaded from RAP-DB (http://rapdb.dna.affrc.go.jp/download/ ; rep_RAP2). Then, all possible CATG + 17nt tag sequences were created from full-length cDNAs and used as reference tag database. Unique tag sequences and their numbers were extracted from our raw DGE tags and these tags were aligned against the reference tag database using SOAP. Only perfect matches were kept for further analysis, and no mismatches were allowed. Expression level of a gene was represented by the total number of tags that uniquely aligned to the gene. Gene expression levels were normalized to tag number per million tags for gene expression comparisons among different samples.

organism: Oryza sativa

source_name: japonica

extract_protocol: A single young panicle from each of the cultivated rice subspecies and the two wild rice species was ground in liquid nitrogen to fine powder using mortar and pestle. Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen).

tag: subspecies

value: japonica

value: young panicle


title: Nivara DGE analysis

organism: Oryza nivara

source_name: nivara

tag: source

value: wild rice


title: Patient ID_211

source_name: Liver, ID_211


title: -P+3h

description: small RNA

value: P limiting for 3 hours


source_name: PBL of healthy donor P kept in parallel ground conditions (control-1g).

tag: individual

value: donor P

value: 1g condition

tag: sample name

value: Human Peripheral blood lymphocytes (PBL)


title: FN

description: small RNA

value: full nutrition


title: Patient ID_190

source_name: Liver, ID_190

tag: tissue


title: Patient ID_209

source_name: Liver, ID_209


title: Patient ID_210

source_name: Liver, ID_210


title: CTR_1g_B (PBL of healthy donor B, 1g condition)

source_name: PBL of healthy donor B in parallel ground conditions (control-1g).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named B, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes were kept in parallel ground conditions (control-1g).

value: donor B


title: Patient ID_191

source_name: Liver, ID_191

value: liver (chronic hepatitis)


title: Patient ID_195

source_name: Liver, ID_195

value: sustained virological responder


title: Patient ID_205

source_name: Liver, ID_205

value: Male


title: Patient ID_208

source_name: Liver, ID_208


title: Patient ID_194

source_name: Liver, ID_194


title: Patient ID_206

source_name: Liver, ID_206


title: CTR_mmg_B (PBL of healthy donor B, mmg condition)

source_name: PBL of healthy donor B in modelled microgravity (control-mmg).

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named B, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were incubated in modelled microgravity (control-mmg).

value: modeled microgravity (MMG) condition

value: CTR-mmg-B


title: Patient ID_204

source_name: Liver, ID_204

value: non-virological responder

value: Female


title: Patient ID_189

source_name: Liver, ID_189


title: Patient ID_207

source_name: Liver, ID_207


title: Patient ID_192

source_name: Liver, ID_192


title: Patient ID_188

source_name: Liver, ID_188

value: transient virological responder


title: Patient ID_187

source_name: Liver, ID_187


title: IVF1.2 miRNA_Seq

status: Public on Jun 20 2011

city: kunming

first: zhenghua

last: sun

address: jiaochangdong road 32#

institute: kunming institute of zoology.CAS

description: small RNA sequencing data of IVF1.2

data_processing: To obtain clean reads, the original 35nt reads from sequencing were filtered by trimming the 5' and 3' adaptors, getting rid of contaminant, too-small (<18nt) and low-quality reads.

organism: Macaca mulatta

source_name: embryonic stem cells

extract_protocol: Total RNA was extracted from each sample using the mirVana miRNA isolation kit (Ambion). According to the manufacturer's instructions (Illumina), small RNA fraction between 18-30 nt was isolated from total RNA by PAGE purification and ligated with a pair of adaptors to their 5' and 3' ends. Then the small RNA molecules were converted to cDNA by RT-PCR and amplified using the adaptor primers. The purified DNA was used directly for cluster generation and sequencing analysis by the Illumina Genome Analyzer.

value: stem cells

tag: cell line

tag: origin

value: blastocysts

tag: passages


title: Patient ID_160

source_name: Liver, ID_160


title: Patient ID_186

source_name: Liver, ID_186


title: Patient ID_159

source_name: Liver, ID_159


title: Patient ID_158

source_name: Liver, ID_158


title: Patient ID_156

source_name: Liver, ID_156


title: Patient ID_155

source_name: Liver, ID_155


title: Patient ID_157

source_name: Liver, ID_157


title: Patient ID_218

source_name: Liver, ID_218


title: -N

description: small RNA

source_name: Arabidopsis thaliana wild-type seedlings

value: Columbia (Col-0)

value: Nitrogen limiting


title: Patient ID_152

source_name: Liver, ID_152


title: Patient ID_151

source_name: Liver, ID_151


title: Patient ID_154

source_name: Liver, ID_154


title: Patient ID_153

source_name: Liver, ID_153


title: Patient ID_142

source_name: Liver, ID_142


title: Patient ID_145

source_name: Liver, ID_145


title: Patient ID_137

source_name: Liver, ID_137


title: Patient ID_138

source_name: Liver, ID_138


title: Patient ID_140

source_name: Liver, ID_140


title: Patient ID_139

source_name: Liver, ID_139


title: Patient ID_141

source_name: Liver, ID_141


title: Patient ID_150

source_name: Liver, ID_150


title: Patient ID_136

source_name: Liver, ID_136


title: Patient ID_143

source_name: Liver, ID_143


title: Patient ID_144

source_name: Liver, ID_144


title: Patient ID_133

source_name: Liver, ID_133


title: Patient ID_135

source_name: Liver, ID_135


title: Patient ID_134

source_name: Liver, ID_134


title: Patient ID_132

source_name: Liver, ID_132


title: Patient ID_131

source_name: Liver, ID_131


title: Patient ID_128

source_name: Liver, ID_128


title: Patient ID_130

source_name: Liver, ID_130


title: Patient ID_127

source_name: Liver, ID_127


title: Patient ID_122

source_name: Liver, ID_122


title: Patient ID_126

source_name: Liver, ID_126


title: Patient ID_125

source_name: Liver, ID_125


title: Patient ID_121

source_name: Liver, ID_121


title: Patient ID_120

source_name: Liver, ID_120


title: -P

description: small RNA

source_name: Arabidopsis thaliana wild-type seedlings

value: P limiting


title: Patient ID_117

source_name: Liver, ID_117


title: Patient ID_116

source_name: Liver, ID_116


title: Patient ID_119

source_name: Liver, ID_119


title: Patient ID_118

source_name: Liver, ID_118


title: Patient ID_123

source_name: Liver, ID_123


title: Patient ID_114

source_name: Liver, ID_114


title: Patient ID_129

source_name: Liver, ID_129


title: Patient ID_115

source_name: Liver, ID_115


title: Patient ID_124

source_name: Liver, ID_124


title: Patient ID_113

source_name: Liver, ID_113


title: IVF3.2 miRNA_Seq

description: small RNA sequencing data of IVF3.2

source_name: embryonic stem cells


title: Patient ID_109

source_name: Liver, ID_109


title: Patient ID_112

source_name: Liver, ID_112


title: Patient ID_111

source_name: Liver, ID_111


title: Indica DGE analysis

description:
DGE analysis.
anchor: NlaIII
tag length: 21
tag count: 558498

source_name: indica

value: indica

value: young panicle


title: Rufipogon DGE analysis

description:
DGE analysis.
anchor: NlaIII
tag length: 21
tag count: 556909

organism: Oryza rufipogon

source_name: rufipogon

value: wild rice


title: IVF3.3 miRNA_Seq

description: small RNA sequencing data of IVF3.3


title: Patient ID_110

source_name: Liver, ID_110


title: Patient ID_107

source_name: Liver, ID_107


title: original ZFNs DD/RR 10pg monster stage_1_off_target_seq_barcode_CG

status: Public on Aug 25 2010

city: Worcester

first: Scot

last: Wolfe

state: MA

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

description:
48 off-target sites and the target site were PCR amplified using the genomic DNA from the ZFN  treated embryos. The different ZFN treatments were barcoded and sequences belonging to different sites can be binned using 9 bp unique prefix
raw reads, no quality score

library_source: genomic

data_processing: Sequences were categorized into different treatments using the 2bp barcode. Sequences belonging to different off-target sites and the target site were binned using a unique 9 bp nonamer

molecule: genomic DNA

organism: Danio rerio

source_name: original ZFNs DD/RR 10pg Monsters

extract_protocol: The off-target sites were amplified from genomic DNA from  ZFNs treated embryos and pooled together. PCR products from different treatments of ZFNs were barcoed and the pools were amplified using Illumina 1.1 and 2.1 geomic primers.

treatment_protocol: zebrafish embryos at single cell stage were injected with ZFN mRNAs at different doses

tag: developmental stage

value: 24 h old embryos

tag: genotype

value: Wild Type

value: original ZFNs DD/RR 10 pg

tag: phenotype

value: monster


title: Uninjected stage_1_off_target_seq_barcode_TT

source_name: Uninjected

tag: treatment

value: uninjected

value: normal


title: New ZFNs DD/RR 20pg normal stage_1_off_target_seq_barcode_GT

source_name: New ZFNs DD/RR 20pg Normals

value: New ZFNs DD/RR 20 pg


title: Original ZFNs DD/RR 10pg normal stage_1_off_target_seq_barcode_GG

source_name: Original ZFNs DD/RR 10pg Normals

value: Original ZFNs DD/RR 10 pg


title: Patient ID_101

source_name: Liver, ID_101

value: liver (chronic hepatitis)

tag: drug-response

value: transient virological responder

tag: age (years)

value: Male


title: Patient ID_106

source_name: Liver, ID_106

tag: sex

value: Female

tag: type of hcv


title: Patient ID_105

source_name: Liver, ID_105

value: non-virological responder

tag: degree of inflammation/fibrosis


title: Patient ID_103

source_name: Liver, ID_103

value: sustained virological responder


title: Patient ID_102

source_name: Liver, ID_102


title: rrf-3_mRNA

status: Public on Feb 01 2010

first: Ayelet

last: Lamm

address: 300 Pasteur Drive, Lane Bldg Room L302

department: Pathology

institute: Stanford University School of Medicine

data_processing: The processed data files in fasta format contain the parsed small RNA reads for each sample (without 5' barcode sequence or 3' adapter sequences). The raw files each correspond to a single lane of sequence sequences; however, multiple samples were present in each lane. Each sample was barcoded with a 3 or 4 nt sequence at the 5’ end, such that the first letter of each read is the first letter of the barcode. Since the small RNAs were ~22 nt in length and 36 nucleotides were sequenced, most of the reads also contain a short stretch of the 3’ adapter sequence at the 3’ end. Custom-built Java scripts were used to sort the reads according to their barcodes and to trim off both the barcodes and 3’ adapter to produce the small RNA processed data files. The start of the 3’ adapter was recognized by the 3’-most instance of it’s first four nucleotides, “CTGT”. The polyA RNA processed data files are slightly different in that the RNA fragments were > 100 nt in length such that the 3’ adapter was not included in the 36 nt reads. Hence, only the 5’ barcode was trimmed off for these samples.

source_name: whole L4 hermaphrodite

extract_protocol: Intact small RNA or fragmented polyA RNA was first ligated to an adenylated 3' adapter (IDT linker 1). In the case of polyA RNA and 5'-P-dependent small RNA, the samples were then ligated to a barcoded 5' adapter. In the case of 5'-P-independent small RNA, the sample were first treated with Antarctic phosphatase then T4 Polynucleotide Kinase before ligating to a barcoded 5' adapter. Subsequently, all samples were reverse transcribed using a primer complementary to the 3' adapter, then PCR amplified with primers carrying extrensions to add the the Illumina primer sites.

tag: strain

tag: growth temperature (°c)

tag: small rna capture method

tag: final rna type

value: polyA RNA


title: New ZFNs DD/RR 10pg normal stage_1_off_target_seq_barcode_TG

source_name: New ZFNs DD/RR 10pg Normals

value: New ZFNs DD/RR 10 pg


title: N2_mRNA

value: wild type


title: New ZFNs DD/RR 20pg monster stage_1_off_target_seq_barcode_CT

source_name: New ZFNs DD/RR 20pg Monsters

value: 24 h old embryos


title: Original ZFNs DD/RR 20pg monster stage_1_off_target_seq_barcode_AT

source_name: Original ZFNs DD/RR 20pg Monsters

value: Wild Type

value: Original ZFNs DD/RR 20 pg


title: rrf-3_sperm_P-dependent

source_name: isolated spermatogenic cells

value: small RNA


title: control_sperm_P-dependent


title: Patient ID_104

source_name: Liver, ID_104

tag: tissue


title: dcr-1_P-dependent


title: eri-9_P-dependent


title: ergo-1_P-dependent


title: eri-1_P-dependent


title: fem-1_P-independent

source_name: whole adult hermaphrodite


title: dcr-1_P-independent


title: glp-4_P-independent


title: newborn_rep10

status: Public on Apr 26 2010

city: Cambridge

first: H. Rosaria

last: Chiang

address: 9 Cambridge Center

department: Biology

institute: MIT/Whitehad Institute

description: sample name: FC5282.7

data_processing: Small RNA sequences 16-27 nt long are provided with the number of reads for each unique sequence. Small RNA 5p ends were observed as the 5p end of the Illumina read. Small RNA 3p ends were determined using matches to ligated linker sequences.

source_name: newborn

extract_protocol: The small RNA cDNA libraries were made as described (Grimson et al. 2008), except for the 3' adaptor ligation, which was 5' adenylated pTCGTATGCCGTCTTCTGCTTGidT. For a detailed protocol, see http://web.wi.mit.edu/bartel/pub/protocols.html.

value: whole newborn

tag: molecule


title: dorsal SKPs sample 2

status: Public on Sep 03 2010

city: Toronto

first: Freda

last: Miller

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

description: RMA expression value derived from Expression Console software; gene-core analysis

hyb_protocol: Samples were hybridized with GeneChip Rat Gene 1.0 ST Arrays (Affymetrix) and scanned at the HSC Microarray Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were background corrected and normalized using standard RMA procedure implemented in the Affymetrix Expression Console software. The preprocessed data were analyzed using the LIMMA Bioconductor package to identify genes that show significant evidence of differential expression between SKPs and MSCs.

organism: Rattus norvegicus

source_name: dorsal SKPs sample 2

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol (Invitrogen), as per the manufacturer’s instructions, followed by the RNeasy Mini Kit (Qiagen).

tag: cell passage

value: twiced-passaged cells

value: Sprague Dawley

tag: cell type

value: dorsal SKPs


title: ergo-1_P-independent


title: dorsal SKPs sample 3

source_name: dorsal SKPs sample 3


title: eri-9_P-independent


title: newborn_rep11

description: sample name: FC5282.8


title: eri-1_P-independent


title: rde-1_P-independent


title: dorsal SKPs sample 1

source_name: dorsal SKPs sample 1


title: rde-4_P-independent


title: newborn_rep6

description: sample name: FC5282.2


title: newborn_rep9

description: sample name: FC5282.6


title: rrf-3_P-independent_2


title: newborn_rep8

description: sample name: FC5282.5


title: rrf-3_P-dependent


title: rrf-3_P-independent_1


title: rrf-1_P-dependent


title: N2_P-dependent


title: glp-1_P-independent


title: rrf-1_P-independent


title: N2_P-independent_3


title: N2_P-independent_2


title: N2_P-independent_1


title: Barrett's adenocarcinoma P5708_AH

status: Public on Jan 30 2010

first: Matteo

last: Fassan

state: PD

address: via Gabelli 61

department: Department of Diagnostic Sciences & Special Therapies

hyb_protocol: Hybridization of biotin-labeled complementary DNA was performed on the Ohio State University  miRNA microarray chip OSU_CCC version 4.0, which contains ~1100 miRNA probes, including 326 human and 249 mouse miRNA genes, spotted in duplicates. The hybridized chips were washed and processed to detect biotin-containing transcripts by streptavidin-Alexa647 conjugate and scanned on an Axon 4000B microarray scanner (Axon Instruments, Sunnyvale, CA).

scan_protocol: The microarrays were processed by using a method of direct detection of biotin-containing transcripts by streptavidin-Alexa647 conjugate. Processed slides were then scanned by using the PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at power 80 and PMT 70 setting and a scan resolution of 10 nm. Microarray images were analyzed using GENEPIX PRO 6.0 (Axon Instruments).

data_processing: Average values of the replicate spots of each miRNA were background subtracted, normalized, and further analyzed. Normalization was performed using quantiles. miRNAs that are differentially expressed between breast cancer and gynecomastia were identified using a random-variance t-test. The random-variance t-test is an improvement over the standard separate t-test as it permits sharing information among genes about within-class variation without assuming that all genes have the same variance. Genes were considered statistically significant if their p value was less than 0.01. A stringent significance threshold was used to limit the number of false positive findings.

source_name: Barrett's esophagus

label_protocol: Five μg of total RNA from each sample were reverse-transcribed using biotin end-labeled random-octamer oligonucleotide primer.

extract_protocol: Two 2-mm cores were obtained from paraffin blocks for each case. Tissue samples were deparaffinized with xylene at 50°C for 3 minutes. Total RNA extraction was undertaken using the RecoverAll kit (Ambion Inc, Austin, Tex) according to manufacturer’s instructions.

value: Barrett's esophagus

tag: histology

value: Barrett's adenocarcinoma


title: Barrett's mucosa P5711_AAG

description: Hybridization of biotin-labeled complementary DNA was performed on the Ohio State University  miRNA microarray chip OSU_CCC version 4.0, which contains ~1100 miRNA probes, including 326 human and 249 mouse miRNA genes, spotted in duplicates.

value: Barrett's mucosa


title: Barrett's mucosa P5709_AT


title: Normal esophagus P5703_K

value: Normal esophagus


title: High-grade HG-IEN P5694_AAR

value: high-grade intra-epithelial neoplasia


title: Normal esophagus P5704_B


title: Normal esophagus P5706_O


title: Normal esophagus P5705_L


title: Normal esophagus P5707_T


title: High-grade HG-IEN P5692_AAG


title: Barrett's mucosa P5710_AW


title: Low-grade LG-IEN P5713_AAO

value: low-grade intra-epithelial neoplasia


title: High-grade HG-IEN P5695_AAS


title: High-grade HG-IEN P5696_AAT


title: Low-grade LG-IEN P5712_AAN


title: newborn_rep12

description: sample name: solexa_HCT179


title: High-grade HG-IEN P5691_AAP


title: Low-grade LG-IEN P5687_AAJ


title: Low-grade LG-IEN P5688_AAK


title: Low-grade LG-IEN P5690_AAM


title: Low-grade LG-IEN P5689_AAL


title: FLAG-ago1_siRNA

status: Public on Feb 15 2010

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Normalised wiggle files were created by measuring the number of reads that mapped to each base.  Each read counted 1/n towards each base that it align to, where 'n' is the number of  times a read could be aligned in the genome. .wig files are give for each strand and both strands combined for the wild type and rpd1delta only.

Two additional constructs were mapped, ura4GFP (ura4 gene combined with gfp gene) and GFPHP (two gfp genes that form a hairpin).  A gff file describing these constructs and the fasta files for these contructs are included as supplementary files linked to GSE20330.

organism: Schizosaccharomyces pombe

growth_protocol: Strains were grown in PMG complete to keep the GFP hairpin, which is under the nmt1 promoter, expressed. Standard procedures were used for growth and genetic manipulations (Moreno et al., 1991).

extract_protocol: Total small RNA was obtained by resuspending cells in RNA extraction buffer (50 mM Tris–HCl pH 7.5, 10 mM EDTA pH 8, 100 mM NaCl, 1% SDS), lysed with phenol:chloroform 5:1 and acid washed beads. The soluble fraction was extracted with phenol/chloroform. Small RNA were concentrated by precipitating away large RNAs with 10% polyethylene glycol 8000, 0.5 M NaCl and then by ethanol precipitation. For gel-purified small RNA, 10 to 30-nt siRNAs, from 400 μg of total small RNAs, were excised from a 12% polyacrylamide gel. After elution from the gel (incubation over-night in RNA extraction buffer at 4°), small RNAs were extracted with phenol/chloroform was and precipitated with ethanol, sodium acetate, and glycogen. For Ago1-associated small RNA preparation 10 g of cells were lysed in presence of liquid nitrogen using a mortar grinder (Retsch) for 30 minutes. Extracts were prepared by dilution of the crushed cells in 20 ml lysis buffer (50 mM Hepes-NaOH (pH 7.5), 150 mM NaCl, 1 mM MgCl2, 0.1% NP-40, 5mM DTT, 1x Roche EDTA-free protease inhibitors cocktail, 0.5mM PMSF, 1/100 super RNAsin (Ambion), and filtration through GD/X 1.6 μm (Whatman). Immunoprecipitations were performed using 20 μg of M2 anti-Flag antibody (Sigma F1804) coupled to 4 μL protein G Dynabeads resin (Dynal) for 15 minutes at 4 °C. RNA samples bound to Dynabeads were washed once with lysis buffer and once with lysis buffer with 2 mM MgCl2, treated with 200 ng/ml proteinase K (Sigma), extracted with phenol/chloroform and chloroform. RNA was precipitated with ethanol, sodium acetate, and glycogen. Libraries were prepared of the small RNA according to Illumina's instructions for subsequent cDNA sequencing.

tag: genotype

value: 3xFlag:ago1-KanMX6 ars1::pREP1GFP-HP-LEU2 arg3::ura4- GFP arg11::HphMX6 his3-D1 leu1-32 ura4-D18 ade6-210/216

tag: purification

value: FLAG Immunoprecipitation


title: brain_rep5

description: sample name: solexa_HCT178

source_name: brain

value: brain


title: Barrett's mucosa P5683_AAD


title: Barrett's mucosa P5682_AAC


title: Barrett's mucosa P5684_AAE


title: Barrett's mucosa P5685_AAF


title: Low-grade LG-IEN P5686_AAI


title: Barrett's mucosa P5681_AAA


title: Barrett's mucosa P5680_AY


title: Barrett's mucosa P5679_AX


title: Barrett's adenocarcinoma P5671_AJ


title: Barrett's mucosa P5676_AS


title: Barrett's adenocarcinoma P5674_AP


title: Barrett's mucosa P5677_AU


title: Barrett's adenocarcinoma P5672_AL


title: Barrett's adenocarcinoma P5670_AF


title: Barrett's mucosa P5675_AR


title: Normal esophagus P5667_Q


title: Barrett's adenocarcinoma P5673_AO


title: Normal esophagus P5666_P


title: Barrett's adenocarcinoma P5664_J


title: Normal esophagus P5665_M


title: Normal esophagus P5669_AB


title: Normal esophagus P5668_R


title: glp-4_Terminator_seq_s3

status: Public on Oct 01 2009

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
Terminator
tar file of Illumina *_seq.txt files provided as supplementary file

data_processing: Small RNA sequences longer than 17 nt were mapped to the Caenorhabditis elegans genome (WS192, www.wormbase.org). Sequences that matched tRNA or rRNA sequences were then removed. Only full-length perfect matches were allowed. siRNA-targeted loci were defined as a region containing at least 25 reads per million matching reads. Relative abundance at each locus was determined by calculating (22G-RNAs in mutant(or)IP)/(22G-RNAs in wt+22G-RNAs in mutant(or)IP ).

source_name: adult worms lacking germline

growth_protocol: animals were grown at 20 C for approximately 60h.

extract_protocol: CIP-PNK protocol: RNA was resolved in a 15% polyacrylamide 7M Urea Gel, along with 20 picomoles of RNA standard (18- and 26-nt) in separate lanes. Ethidium Bromide staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and ethanol-precipitated using 20mg of glycogen as the carrier.  Gel purified RNA was treated with 1 Unit/µl of Alkaline Phosphatase, Calf Intestine (NEB) in 100mM NaCl, 50mM Tris-HCl, 10mM MgCl2, 1mM Dithiothreitol, pH 7.9 at 25°C and 1 Unit/µl SuperRNaseIn (Ambion) for 1 hour at 37 °C. After phenol extraction, the gel purified RNA and 1µM of each standard were incubated with 20µM of 3’-end linker, 1 Unit of SuperRNaseIN, 10% DMSO and 3 Units T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2, 6mg/mL BSA, 10mM DTT).  The 3’ ligated products were gel purified and treated with 1 Unit/µl Polynucleotide Kinase in 1x Polynucleotide Kinase buffer (70mM Tris-HCl, 10mM MgCl2, 5mM Dithiothreitol, pH 7.6 at 25°C), 2mM ATP, 1 Unit/µl SuperRNAseIN. After phenol extraction, RNAs were incubated in the presence of 30µM of 5’ adapter oligonucleotide, 1 Unit SuperRNaseIN (Ambion) and 1.5 Units of T4 RNA ligase in ligation buffer (50mM Tris-HCI pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP) and 10% Dimethyl sulfoxide). The ligated products were gel purified as described above and reverse transcribed in a standard 50µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 10% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing platform (Illumina, Inc.)

tag: sample type

value: adult worms lacking germline


title: Barrett's adenocarcinoma P5660_F

institute: University of Padova


title: Barrett's adenocarcinoma P5661_G


title: Barrett's adenocarcinoma P5659_E


title: Normal esophagus P5663_I


title: WT_Terminator_seq_JCC-s2

source_name: gravid adult worms

value: gravid adult worms

value: Wild type N2


title: Barrett's adenocarcinoma P5658_D


title: Normal esophagus P5656_A


title: WT_Terminator_seq_CCM-s2


title: Barrett's mucosa P5678_AV


title: Normal esophagus P5662_H


title: WT_Terminator_seq_CCM-s1


title: drh-3_CIPPNK_seq_s3

description:
CIPPNK
tar file of Illumina *_seq.txt files provided as supplementary file


title: drh-3_CIPPNK_seq_s2


title: Patient ID_108

source_name: Liver, ID_108

value: liver (chronic hepatitis)

tag: drug-response

value: sustained virological responder

value: Male


title: WT_CIPPNK_seq_s1


title: WT_CIPPNK_seq_s2


title: Normal esophagus P5657_C