title: Patient13_RNA-seq

description: WT-RNA-seq


title: Patient9_RNA-seq

status: Public on Apr 03 2012

type: SRA

city: Houston

first: Han

last: Liang

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

country: USA

institute: University of Texas MD Anderson Cancer Center

description: WT-RNA-seq

library_source: transcriptomic

data_processing:
WT-seq short reads were mapped to the human reference genome (hg19) and exon junctions (defined as RefSeq gene annotation) using the ABI BioscopeTM (version 1.21) WT-seq analysis pipeline with default parameters.
The reads mapped to the sequences that were not of biological interest, such as rRNAs, tRNAs, and repetitive elements, were first filtered. Then mapped reads with mapping SOLiD_native_quality ≥10 were defined as uniquely mapped reads and used in the downstream analysis.
The “reads per kilobase of exon per million mapped sequence reads” (RPKM) values of the human RefSeq genes were calculated using the RNA-seq flow in the Partek® Genomics Suite™ (version 6.5 beta, Partek Inc., St. Louis, MO, USA).
For the small RNA-seq dataset, the SOLiD System Small RNA Analysis Pipeline Tool (corona RNA2MAP version 0.50) was used: first, the reads mapped to the sequences of no biological interest were filtered, and then the remaining reads were mapped to annotated mature miRNAs (miRBase 13.0) and the human reference genome (key parameters: seed length = 18, seed error = 2, and maximum number of errors = 4).
MiRNA expression was quantified as reads per million (RPM) of reads mapped to known miRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: GeneExpressionRPKM_30Sample_WT.xls; excel file; gene expression (in terms of RPKM) in 30 samples;
Supplementary_files_format_and_content: miRNAExpressionRPM_25Sample_smRNA.xls; excel file; miRNA expression (in terms of RPM) in 25 samples;

molecule: total RNA

organism: Homo sapiens

source_name: tissue specimen

extract_protocol:
The Miravana Kit (Ambion/Applied Biosystems, Foster City, CA, USA) was used to isolate total RNA according to the vendor’s protocol. The whole-transcriptome-sequencing (WT-seq) and small RNA-seq libraries were prepared using the small RNA expression kit (SREK, PN 4397682) of Applied Biosystems Inc. (ABI), based on SOLiD WT and small RNA standard protocols provided by ABI. The individual prepared “barcode” libraries were quantified and pooled equally together for multiplexing. The sequencing runs were performed on SOLiD v 3.0 for both WT-seq and small RNA-seq
WT-seq samples were sequenced in 1/4 slide per sample using 50-nucleotide (nt) single tags; and small RNA-seq samples were sequenced in 1/10 slide per sample using 35-nt single tags.

tag: gender

value: M

tag: age

tag: Stage

value: I

tag: histologics

value: Intestine


title: Wholeflies_w1118_Female_R3_SOLiD_b

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: Flowcell 2; Same poly A mRNA prep used for microarray hybridization

data_processing: High quality reads were matched to individual samples based on the 10 bp bar code tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1. We used only the forward read and trimmed these reads from 50 to 36 bp based on analysis of read quality. Trimmed reads were mapped with Bowtie.  The dm3 from the UCSC Genome Browser which corresponds to the April 2006 Drosophila melanogaster draft assembly from the Berkeley Drosophila Genome Project (Release 5) plus sequences of the 96 synthetic RNAs were used to build a reference index for mapping colorspace data. The reference index was created using the bowtie-build function with default parameters for colorspace. Reads were mapped using -v 2 -m 1 in Bowtie v. 0.12.7 and then unique mapping sequences that mapped to spike-in controls and Flybase gene models were counted using the union mode in HTSeq. Technical replicates for each sample were highly comparable and we pooled reads between the two flow cells for each sample.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Whole flies, 5 day mated adults

growth_protocol: Flies were grown under constant light, temperature, and humidity (25°C; 60% relative humidity) on San Diego Stock Center cornmeal media (DSSC, 2008)

extract_protocol:
The spike-in control mixtures were designed to assess technical performance of a typical gene expression experiment examining enrichment between two conditions. These mixtures consist of the 96 distinct control RNAs from the ERCC (External RNA Control Consortium) project. The RNAs were synthesized, purified, and mixed at NIST. The mixtures (Mix 1 and Mix 2) contain 3 subsets of 32 RNAs: one subset at equal abundance in Mix 1 and Mix 2, representing a “no-change” control; one subset at 1.5 fold enrichment in Mix 1 relative to Mix 2; and another subset at 1.5 fold enrichment in Mix 2 relative to Mix 1. Each subset of 32 control RNAs was designed to span a concentration dynamic range of 220, or 1048576:1. The control IDs and concentrations in Mix 1 and Mix 2 are annotated in the supplementary file linked to the GSE31401 record.
ERCC Spike-in Mix 1 was combined with the diploid control mRNA samples (female and male w1118) and ERCC Spike-in Mix 2 was combined with mRNA from all other DrosDel samples at about 10% concentration the total quantity of mRNA.
Approximately 150-200 ng of polyA selected mRNA was converted to cDNA, using the SOLiDTM Total RNA-Seq Kit PN 4445374 and accompanying kit protocol PN4452437 Rev. A (Life Technologies, Carlsbad, CA). RNA was enzymatically fragmented with RNase III using stated protocol methods and kit supplied components. The fragmented RNA was then cleaned and concentrated using the RiboMinusTM Concentration Module (Invitrogen Corporation, Carlsbad, CA) and eluted in 12 u L of nuclease-free water. The fragmented RNA was then assessed for size distribution and concentration on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with the RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA) and the Qubit® RNA assay (Invitrogen Corporation, Carlsbad, CA), respectively. Fragment distributions were found to have a mean distribution of approximately 150 nts. In preparation for library construction the RNA needed to be sufficiently concentrated such that less than or equal to  3u L of fragmented RNA contained 50 ng. Concentration was performed in a SpeedVac® Concentrator (Savant Instruments Inc., Holbrook, NY) under vacuum and medium heat for approximately 10 minutes. Each dried fragmented RNA sample was then rehydrated to a final concentration of 17 ng/u L in nuclease-free water. Hybridization and ligation of partial P1 adaptor and internal adaptor, at the 5' or 3' end respectively, was performed using concentrated fragmented RNA and kit supplied adaptors and hybridization mixtures. Reverse transcription was then performed as directed by protocol with kit supplied ArrayScriptTM Reverse Transcriptase (Ambion Inc., Austin, TX) and necessary reaction components. Resulting cDNA was then purified using the MinElute® PCR Purification Kit (Qiagen Inc., Valencia, CA) and eluted in 10 u L of Buffer EB supplied by the purification kit. cDNA libraries were then size selected for 150-250 nts fragments that represent cDNA with target sequence and 5' and 3' SOLiDTM sequencing adaptors. The cDNA was run on a Novex® 6% TBE-Urea Gel 1.0 mM (Invitrogen Corporation, Carlsbad, CA) using the XCell SureLockTM Mini-Cell system (Invitrogen Corporation, Carlsbad, CA) to separate the constituent sizes of cDNA. Samples and ladder were loaded on to gel, separated by a lane to minimize cross contamination, and run at 180 V for approximately 30 minutes. The gels were then stained in 50 u L of 1X SYBR Gold nucleic acid gel stain (Invitrogen Corporation, Carlsbad, CA) solution prepared with 1X TBE Running Buffer. Gel and stain were agitated in the dark at room temperature for 10 minutes then imaged with blue-light transilluminator. Using a clean razor blade for each cut the targeted size range of 150-250 nts was excised and, with vertical orientation maintained, vertically cut into four ~ 1mm x 6mm slices. Two of the four slices were used in amplification while the remaining two slices were stored for future use, if necessary, at -20°C. In-gel Polymerase Chain Reaction (PCR) amplification was then performed using excised gel slices and reaction components and primers supplied by the kit. The primers supplied extend and complete the P1 adaptor at the 5' end while primers containing unique barcodes were used to add a unique barcode and P2 adaptor to the 3' end. All samples were uniquely barcoded using the SOLiDTM RNA Barcoding Kit, Modules 17-32 (Life Technologies, Carlsbad, CA). Samples were amplified with AmpliTaq® DNA Polymerase (Applied Biosystems, Carlsbad, CA) using thermal cycling parameters designated by the kit protocol on a PTC-200 DNA Engine (MJ Research, Watertown, MA) for 15 cycles to avoid overamplification. Amplified samples were purified using the PureLink PCR Micro Kit (Invitrogen, Carlsbad, CA). Samples were eluted in 20 u L of Elution Buffer supplied with the purification kit. Following barcoding and amplification, completed cDNA libraries were assessed for size distribution and yield on the 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA). A smear analysis was performed and confirmed <20% of resulting cDNA was smaller than 200 nucleotides and therefore appropriate for templated bead preparation. Individual cDNA libraries were quantified using quantitative PCR (qPCR) on a 7900 HT Real-Time PCR System (Life Technologies, Carlsbad, CA) and pooled with other barcoded samples to create an equimolar pool. Pooled libraries were quantified using qPCR to confirm final molar concentration for use in templated bead preparation. Templated beads were prepared with emulsion polymerase chain reaction (ePCR) using the Applied Biosystems EZ Bead System (Life Technologies, Carlsbad, CA). Two library titration points, 0.4 and 0.8 pM, were initially used for work flow analysis (WFA) to determine input for full ePCR. Upon completion of WFA run on the SOLiDTM v4 instrument it was determined that a 0.6 pM titration point would be used in templated bead preparation to achieve maximum yield of high quality (greather than or equal to  77% On-Axis, less than or equal to 7% Noise to Signal) P2 enriched beads. Samples were run in duplicate in quads on two flow cells of a SOLiDTM v4 platform using ToP chemistry to generate paired-end reads of 50 base pair forward, 35 base pair reverse and a 10 base pair barcode.

treatment_protocol: We collected replicates for experiments by outcrossing the balancer chromosome with the original wild-type stock (w1118) as follows; 18-24 vials were setup with 15 less than 8 day old virgin w1118 females paired with 5 less than 8 day old males of a particular deficiency line per vial. Df/+ female and males were placed together in vials at less than 60 per vial and then aged for five days. On day five, flies were anesthetized with CO2, sorted into males and females, then placed into 1.5 ml Eppendorf tubes and flash frozen on dry ice. All flies aged together for 5 days constituted a replicate. Flash frozen flies were stored in -80°C before RNA extraction.

value: Female

tag: strain

tag: tissue

value: whole flies

tag: developmental stage

value: 5 day old mated adults


title: Wholeflies_w1118_Female_R3_SOLiD_a

description: Flowcell 1; Same poly A mRNA prep used for microarray hybridization


title: Patient6_RNA-seq

description: WT-RNA-seq

value: IV

value: Diffuse


title: Patient10_RNA-seq

description: WT-RNA-seq

value: Normal


title: Patient4_RNA-seq

description: WT-RNA-seq

value: III


title: Patient15_RNA-seq

description: WT-RNA-seq


title: Patient7_RNA-seq

description: WT-RNA-seq


title: Patient8_RNA-seq

description: WT-RNA-seq

value: F


title: Patient21_RNA-seq

description: WT-RNA-seq


title: Patient3_RNA-seq

description: WT-RNA-seq


title: Patient1_RNA-seq

description: WT-RNA-seq

value: Mixed


title: Patient2_RNA-seq

description: WT-RNA-seq


title: EspR_ChIP-Seq_1

status: Public on Apr 02 2012

city: Lausanne

first: Benjamin

last: Blasco

address: Station 19

department: SV-GHI

country: Switzerland

institute: EPFL

description:
Chromatin IP against EspR
The rat anti-EspR antibody was produced by our collaborator Ida Rosenkrands at the STATENS SERUM INSTITUT (Danemark).

library_source: genomic

data_processing:
Alignment: Sequence reads were aligned to the Mtb H37Rv genome (NCBI accession NC_000962.2) using the Bowtie software
Reads from the two experimental replicates were pooled together as they showed a high level of correlation. Reads mapped to the forward and reverse strands were shifted (by 80 bp) and combined together to generate a single merged profile ["EspR_merged.bed" available as a Series Supplementary file].  In order to estimate the binding location in the enriched regions, we used a deconvolution algorithm that models the expected tag distribution on both strands.
Genome Build:
EspR1.bed: NC_000962.2

molecule: genomic DNA

organism: Mycobacterium tuberculosis

source_name: log phase_Mtb H37Rv_EspR_ChIP

growth_protocol: Mtb H37Rv cultures (50 ml) were grown to OD600 0.4-0.6 in complete 7H9 medium

extract_protocol: Crosslinked bacteria cells were sonicated and protein-DNA complexes were isolated with an anti-EspR antibody. Libraries were prepared according to Illumina's instructions.

treatment_protocol: Bacteria cells were treated with formaldehyde (final concentration 1%) for 10 min at 37°C

tag: growth phase

value: mid-log

tag: chip antibody

value: rat anti-EspR


title: EspR_ChIP-Seq_2

data_processing:
Alignment: Sequence reads were aligned to the Mtb H37Rv genome (NCBI accession NC_000962.2) using the Bowtie software
Reads from the two experimental replicates were pooled together as they showed a high level of correlation. Reads mapped to the forward and reverse strands were shifted (by 80 bp) and combined together to generate a single merged profile ["EspR_merged.bed" available as a Series Supplementary file].  In order to estimate the binding location in the enriched regions, we used a deconvolution algorithm that models the expected tag distribution on both strands.
Genome Build:
EspR2.bed: NC_000962.2


title: Input_DNA

description: input DNA

data_processing:
Alignment: Sequence reads were aligned to the Mtb H37Rv genome (NCBI accession NC_000962.2) using the Bowtie software
Reads from the two experimental replicates were pooled together as they showed a high level of correlation. Reads mapped to the forward and reverse strands were shifted (by 80 bp) and combined together to generate a single merged profile ["EspR_merged.bed" available as a Series Supplementary file].  In order to estimate the binding location in the enriched regions, we used a deconvolution algorithm that models the expected tag distribution on both strands.
Genome Build:
Input_DNA.bedgraph: NC_000962.2

source_name: log phase_Mtb H37Rv_input control


title: NBM_16

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

description: monoclonal antibody to precipitate 5 methyl cytosine

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome (build 36, March 2006) using the softwares 'maq' (http://maq.sf.net/) and 'Bowtie' (http://bowtie-bio.sourceforge.net/index.shtml).
DNA Methylation: Absolute DNAm states were inferred from alignment of raw reads using the Batman algorithm (Down et al., Nat Biotech 2008)

source_name: Bone marrow

growth_protocol: Genomic DNA was extracted from AML by Qiagen kit, then the DNA sonicated by Sonic vibracel. The DNA frament will be blunt ended by adding klenow enzme and T4 polynucleotide kinase

extract_protocol: The quantified dsDNA MeDIP library was prepared for sequencing over Illumina flow cell. Preparation for sequencing includes firstly, DNA denaturation by NaOH solution and further diluted in HT1 buffer (tris buffer) to end into 4 PM concentration solution ready to be put over the flow cell. Secondly, the 'cluster generation' step, which is processed by adding a mixture of unlabelled nucleotides and DNA polymerase to the ssDNA library, which will attach to the primer sequences present inside the surface of the flow cell.  The result is initiating the amplification of each fragment through a 'bridge amplification' reaction, which is unique to Illumina and subsequently generation of millions of clusters; each one represents a single fragment of MeDIP library. The average insert size of paired-end libraries was 200 bp and the standard deviation was of 20 bp. Illumina GAII, with the criteria of 1.4-pipeline software and 2.4-system control software (SCS) can produce 180.000-270.000 clusters/tile

treatment_protocol: 7.5 μl of monoclonal antibody (Diagenode 1μg/μl) is added to at least 4 μg of DNA for 2 hours at 4C with slow rotation. 40 µl of magnetic Dynabeads (Dynabeads M-280 sheep anti-Mouse IgG, Invitrogen) are prewashed with 1ml 1XIP buffer and collected with a magnetic rack. Dynabeads are added to the DNA sample and incubated for 2 hours at 4C with slow rotation. Dynabeads are collected using a magnet and washed with 750 µl 1X IP buffer for three times. To release the immunoprecipitated DNA, Dynabeads are resuspended in 200 µl digestion buffer and 5 µl of Proteinase Kinase (10mg/ml). The suspension is incubated for 2 hours at 55°C with shaking to avoid the sedimentation of the beads. After the incubation, the sample is divided in 2 separate tubes and purified by Zymo DNA Clean and Concentrator-5 kit (using 700 µl binding buffer) in 20 µl EB. 10 µl MeDIP and 10 ng of input DNA are subjected to limited PCR (LM PCR) using primers provided from Illumina for paired end library preparation. For size selection, 15 µl of MeDIP is run over 2% low melting temperature gel. MeDIP is excised from gel in the range of 250-300 bp and eluted in 30 µl EB using Qiagen Gel Extraction kit.

tag: cytogenetic

value: control NBM

tag: sample type

value: DNA of a healthy donor

tag: medip antibody

value: 5- methyl cytosine (Diagenode.sa, MAb-081-100, Lot/batch DA-0016)


title: Patient5_RNA-seq

description: WT-RNA-seq

value: II


title: NBM_14


title: AML_11

source_name: PB (peripheral blood)

value: trisomy 8

value: DNA of AML patient


title: NBM_15

value: DNA of non infiltering follicular lymphoma patient


title: AML_8


title: NBM_13


title: AML_10


title: AML_12


title: AML_7


title: AML_6

value: Normal karyotype (NK)


title: AML_5


title: AML_3


title: AML_2


title: AML_1


title: AML_4


title: HK2 cells untreated; 48hrs rep1

status: Public on Apr 01 2012

city: Dublin

first: Melissa

middle: J

last: Morine

address: Belfield

country: Ireland

institute: University College Dublin

description: Gene expression data from untreated hk2 cells, t=48hrs.

data_processing: Alignment: Sequence reads were mapped to the hg18 build of the human genome using the Bowtie software. All reads mapping to the genome with two or fewer mismatches were retained.

source_name: HK-2 cells

growth_protocol: HK-2 cells were cultured at 37 degC in a humidified atmosphere of 95% air/5% CO2, and maintained in DMEM-F12 supplemented with 2 mM L-glutamine, 100 U/ml penicillin, 100 ug/ml streptomycin, 10 ng/ml EGF, 36 ng/ml hydrocortisone, 4 pg/ml triiodothyronine and 5 ug/ml insulin-transferrin-selenium solution. Cells were subcultured using trypsin-EDTA at a ratio of 1:5.

extract_protocol: The Illumina library was prepared according to the manufacturer's instructions. poly (A) mRNA was isolated from 6 Âµg of total RNA using Dynal oligo (dT) beads (Invitrogen). Zinc-mediated fragmentation of mRNA was performed using an RNA fragmentation kit (Ambion), followed by first- and second-strand cDNA synthesis using random hexamer primers. End-repair reaction was performed with T4 DNA polymerase and E.coli DNA polymerase I Klenow Fragment. 'A' nucleotide addition was performed using 3'-to-5' exo-nuclease, followed by adapter ligation using T4 DNA ligase. 200 bp fragements were gel purified using a QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. Library quantitation was performed using a Qubit(tm) Flurometer and HS dsDNA kit (Invitrogen). Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: HK-2 cells were plated in triplicate for stimulation with TGF-beta1 for 0 or 48 h.  This experiment was carried out three times on different days, with triplicate samples for each time point being pooled on each occasion.

tag: cell line

tag: cell type

value: kidney proximal tubule epithelial cell line


title: HK2 cells untreated; 48hrs rep3


title: HK2 cells untreated; 48hrs rep2


title: HK2 cells TGF-beta1; 48hrs rep1

description: Gene expression data from hk2 cells treated with TGF-beta1, t=48hrs.


title: Chlamydomonas reinhardtii 4A+ wild-type

city: Dübendorf

first: Beat

middle: B

last: Fischer

address: Ueberlandstr. 133

department: Department of Environmental Toxicology

institute: Eawag

description:
Illumina's RNA-Seq whole transcriptome analysis
poly-A purification, random fragmentation

library_source: non-genomic

data_processing:
Processed sequence files from the Solexa pipeline output were aligned against the v.3.1 assembly of the Chlamydomonas genome. The SOAP alignment program (Li et al., 2008) was used to map the short reads in two steps. In a first alignment round, the raw sequences were aligned to the genomic sequence with a tolerance of up to two mismatches and no indels. For those sequences that did not align to the genome a second round alignment was performed in which we recursively trim one base at a time (up to 21-mers or half of the read length) at either the 5’ or 3’ end of the reads until we found a (perfect) match to the genome.
Alignments from both rounds were tagged as either unique or not unique and combined. The most 5’ position of each alignment is recorded along with the length of the alignment. For differential expression analysis, per-base unique hits from both strands were pooled and summed across the genome to obtain gene counts. Additional normalization was performed to estimate gene expression levels.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: The strains were grown mixotrophically in a Tris-acetate phosphate (TAP) medium at 25°C and 100 μmol photons m-2 s-1 photosynthetically active radiation (PAR) in a 12 h day night cycle.

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 at Illumina by whole transcriptome analysis.

treatment_protocol: Cells of cultures grown in 12 h light dark cycles for several days were adjusted to 2×106 cells ml-1 at the beginning of the dark cycle and the cells were collected 6 h after the lights came on from three independent biological replicates.

tag: genotype

value: wild type

tag: medium

value: TAP

tag: sequencing cycles / read length

tag: library type

value: single-end


title: Sox10 rep2 ChIP

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing: Basecalling was performed using the standard Illumina Pipeline.  Reads were mapped to the Rattus norvegicus genome (Rn4) using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis. Peak finding was performed using the R package MOSAiCS (31) controlling the false discovery rate at 0.05. MOSAiCS implements a model-based approach where the background distribution for unbound regions take into account systematic biases such as mappability and GC content and the peak regions are described with a two component Negative Binomial mixture model. MOSAiCS is available at www.bioconductor.org/packages/2.8/bioc/vignettes/mosaics/inst/doc/mosaics-example.pdf.

organism: Rattus norvegicus

source_name: sciatic nerve at P15

extract_protocol: ChIP samples ranging in total quantity from 1.3ng (Egr2) - 6.8ng (Sox10), along with 10ng of input controls, were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation.   All libraries were generated using reagents from either the Illumina Paired End Sample Preparation Kit (Illumina Inc., San Diego, CA, USA) or the NEBNext® DNA Sample Prep Reagent Set 1 (New England Biolabs, Ipswitch, MA, USA) and the Illumina protocol "Preparing Samples for ChIP Sequencing of DNA" (Illumina part # 11257047 RevA) as per the manufacturer's instructions but with the following modification: products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen, Carlsbad, California, USA) targeting either 275bp fragments (Egr2) or 200-400bp fragments (Sox10, Sox10 input).  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent Technologies, Santa Clara, CA, USA) and QuantIT PicoGreen dsDNA Kit (Invitrogen, Carlsbad, California, USA), respectively, and libraries were standardized to 10 micromolar.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  A single read, 36 bp run was performed, using standard 36 bp SBS kits (v4) and either SCS 2.6 or 2.8 software on an Illumina Genome Analyzer IIx.

treatment_protocol: ChIP assays were performed on pooled sciatic nerves from Sprague-Dawley rat pups at postnatal day 15 as previously described (Jang et al., 2006) except that for the EGR2 ChIP, immunoprecipitation was carried out using Dynabeads® Protein AG Mix (Invitrogen) in lysis buffer containing 1% TritonX-100 instead of 0.3% TritonX-100. Herring sperm DNA was omitted from the blocking procedure. The antibodies used in this study include SOX10 (Santa Cruz Biotechnology, sc-17342x), and EGR2 (Abcam).

value: Schwann cells

value: Spague-Dawley


title: Sox10 rep1 ChIP lane 2

source_name: sciatic nerve at P16

value: SOX10 (Santa Cruz Biotechnology, sc-17342x)


title: AML_9


title: Sox10 rep1 ChIP lane 1


title: Egr2 rep2 input


title: Egr2 rep2 ChIP

value: EGR2 (Abcam)


title: Egr2 rep1 input


title: Egr2 rep1 ChIP


title: HK2 cells TGF-beta1; 48hrs rep2


title: KO library 3

city: St Lucia

first: Michael

middle: Robert

last: Tallack

state: QLD

address: Services Road

country: Australia

institute: Institute for Molecular Bioscience, The University of Queensland

data_processing:
s_5.bam; genome build: mm9
The six files of raw mRNA-Seq reads were mapped onto the mm9 genome of UCSC (ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/mm9.ebwt.zip) to generate six BAM files individually using Tophat-1.3.1 (http://tophat.cbcb.umd.edu/downloads/).

organism: Mus musculus

source_name: Total fetal Liver Klf1-/-

growth_protocol: Fetal livers were collected from E14.5 timed matings (Klf1+/- x Klf1+/-) by dissection, mechanically dissociated and passed through a 40 micron cell strainer to obtain a single cell suspension. Fetal livers were collected from 3 Klf1-/- embryos and 3 Klf1+/+ embryos from 2 independent litters and genotypes confirmed by PCR.

extract_protocol: Total RNA was collected from homogenized E14.5 fetal livers using TRIzol (Invitrogen) and treated with amplification grade DNaseI (Invitrogen). 12μg of total RNA for each sample was treated with the mouse GlobinClear kit (Ambion) to remove the majority of globin RNA. Libraries were prepared from this RNA starting with 8μg per sample and using the mRNA-seq Sample Prep Kit (Illumina) as per recommended instructions. Cluster generation and sequencing was performed as per standard Illumina GAIIx protocols to generate single end reads of 76bp. Each library was sequenced in an individual lane of the GAIIx flow cell. A single Klf1+/+ library (WT library 3) was sequenced to approximately twice the depth by generating two lanes of sequence.

value: BALB/c

tag: genotype/variation

value: Fetal liver

value: Embryonic day 14.5


title: KO library 2

data_processing:
s_3.bam; genome build: mm9
The six files of raw mRNA-Seq reads were mapped onto the mm9 genome of UCSC (ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/mm9.ebwt.zip) to generate six BAM files individually using Tophat-1.3.1 (http://tophat.cbcb.umd.edu/downloads/).


title: KO library 1

data_processing:
s_2.bam; genome build: mm9
The six files of raw mRNA-Seq reads were mapped onto the mm9 genome of UCSC (ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/mm9.ebwt.zip) to generate six BAM files individually using Tophat-1.3.1 (http://tophat.cbcb.umd.edu/downloads/).


title: WT library 3

data_processing:
s_1_8.bam; genome build: mm9
The six files of raw mRNA-Seq reads were mapped onto the mm9 genome of UCSC (ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/mm9.ebwt.zip) to generate six BAM files individually using Tophat-1.3.1 (http://tophat.cbcb.umd.edu/downloads/).

source_name: Total Fetal Liver Klf1+/+

value: wildtype


title: WT library 2

data_processing:
s_7.bam; genome build: mm9
The six files of raw mRNA-Seq reads were mapped onto the mm9 genome of UCSC (ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/mm9.ebwt.zip) to generate six BAM files individually using Tophat-1.3.1 (http://tophat.cbcb.umd.edu/downloads/).


title: E. coli recoded ompF (recoded ompF gene)

city: San Francisco

first: Gene-Wei

last: Li

state: CA

address: 1700 4th Street, BH404

institute: UCSF

description:
Ribosome-protected mRNA
Ecoli_ompF_recoded

data_processing:
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
Genome Build:
OmpFrecode_f.wig: NC_000913.2
OmpFrecode_r.wig: NC_000913.2

organism: Escherichia coli

source_name: E. coli recoded ompF

extract_protocol: Ribosome protected mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)

tag: treatment

value: Ribosome-protected mRNA, Ribosome footprint sample digested with 60 units of micrococcal nuclease per A260 absorbance

value: BJW9 w/ recoded ompF

value: MOPS


title: WT library 1

data_processing:
s_6.bam; genome build: mm9
The six files of raw mRNA-Seq reads were mapped onto the mm9 genome of UCSC (ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/mm9.ebwt.zip) to generate six BAM files individually using Tophat-1.3.1 (http://tophat.cbcb.umd.edu/downloads/).


title: E. coli OlacZ (orthogonal ribosomes and  orthogonal lacZ mRNA)

description:
Ribosome-protected mRNA
Ecoli_Oribosome_OlacZ

data_processing:
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
Genome Build:
OlacZ_f.wig: NC_000913.2
OlacZ_r.wig: NC_000913.2

organism: Escherichia coli BW25113

source_name: E. coli OlacZ

value: BW25113 w/ orthogonal ribosome and orthogonal lacZ

tag: plasmid


title: B. sub 168 60 units of MNase rep2

description:
Ribosome-protected mRNA
Bsub_60UMNase_perA260_replicate2

data_processing:
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
Genome Build:
Bsub_111025_f.wig: NC_000964.3
Bsub_111025_r.wig: NC_000964.3

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: B. sub 168

value: Ribosome-protected mRNA by Ribosome footprint sample digested by 60 units of  micrococcal nuclease per A260 absorbance

tag: strain

value: LB


title: SFFV.miR-511-3p-mut_TAMs_003

city: Oslo

first: Camilla

last: Stormo

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: Oslo University Hospital

data_processing:
308R5.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).

source_name: F4/80+ tumor-associated macrophages (TAMs) overexpressing mutated miR-511-3p (miR-511-3p-mut), isolated from Lewis Lung Carcinoma

extract_protocol: Libraries were prepared according to Illumina TruSeq RNA sample preparation guide Part# 15008136 Rev.A. RNA fragmentation with “Elute, Prime, Fragment Mix” was performed for 4 minutes at 94 oC.


title: SFFV.miR-511-3p-mut_TAMs_002

data_processing:
307R5.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).

value: F4/80+ tumor-associated macrophages (TAMs) overexpressing mutated miR-511-3p (miR-511-3p-mut)


title: B. sub 168 30 units of MNase

description:
Ribosome-protected mRNA
Bsub_30UMNase_perA260

data_processing:
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
Genome Build:
Bsub_110411_30_f.wig: NC_000964.3
Bsub_110411_30_r.wig: NC_000964.3

value: Ribosome-protected mRNA by Ribosome footprint sample digested by 30 units of  micrococcal nuclease per A260 absorbance


title: SFFV.miR-511-3p_TAMs_002

data_processing:
311R5.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).

source_name: F4/80+ tumor-associated macrophages (TAMs) overexpressing miR-511-3p, isolated from Lewis Lung Carcinoma


title: SFFV.miR-511-3p_TAMs_003

data_processing:
312R5.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).

value: F4/80+ tumor-associated macrophages (TAMs) overexpressing miR-511-3p


title: CD11c+TAMs_003

data_processing:
TAM3.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).

source_name: F4/80+CD11c+ tumor-associated macrophages (TAMs) isolated from Lewis Lung Carcinoma


title: SFFV.miR-511-3p-mut_TAMs_001

data_processing:
306R5.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).


title: SFFV.miR-511-3p_TAMs_001

data_processing:
309R5.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).


title: CD11c+TAMs_002

data_processing:
TAM2.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).


title: CD11c+TAMs_001

data_processing:
TAM1.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).


title: MRC1+TAMs_001

data_processing:
TEM1.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).

source_name: F4/80+MRC1+ tumor-associated macrophages (TAMs) isolated from Lewis Lung Carcinoma


title: B. sub 168 60 units of MNase rep1

description:
Ribosome-protected mRNA
Bsub_60UMNase_perA260_replicate1

data_processing:
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
Genome Build:
Bsub_110411_60_f.wig: NC_000964.3
Bsub_110411_60_r.wig: NC_000964.3


title: MRC1+TAMs_002

data_processing:
TEM2.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).


title: E. coli MG1655 rep2

description:
Ribosome-protected mRNA
Ecoli_replicate2

data_processing:
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
Genome Build:
Ecoli_111101_D_f.wig: NC_000913.2
Ecoli_111101_D_r.wig: NC_000913.2

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655


title: MRC1+TAMs_003

data_processing:
TEM3.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).


title: E. coli MG1655 rep1

description:
Ribosome-protected mRNA
Ecoli_replicate1

data_processing:
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
Genome Build:
Ecoli_111101_C_f.wig: NC_000913.2
Ecoli_111101_C_r.wig: NC_000913.2


title: Lvp

city: Blacksburg

first: Zach

middle: N.

last: Adelman

state: VA

address: 305 Fralin Life Science Institute

department: Entomology

institute: Virginia Tech

description: 18-30nt small RNA

data_processing:
small RNAs were mapped to the Ae. aegypti genome using Bowtie allowing for a single mismatch.
Genome Build:
Lvp_unique_mapping_raw_reads.txt: AaegL1.2, September 2009

organism: Aedes aegypti

source_name: Whole adult female

growth_protocol: Mosquitoes were reared in an insectary at 28C and 70% humidity, with a light cycle of 14:10 light:dark.

extract_protocol: Librarys were constructed using Illumina's small RNA library kit. Small RNAs were PAGE purified prior to library construction.

treatment_protocol: Mosquitoes were intrathoracically inoculated with 0.5 ul of a 10^6 PFU/ml suspension of the indicated virus.

tag: age

value: 4 days post emergence

tag: infection

value: no


title: Protonemata dcl4

city: University Park

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

data_processing: Barcoded samples were first parsed to separate different samples mixed in the same run.  Barcode-sorted colorspace reads (35 colors) were then parsed to identify the first five nucleotides of the constant 3' adapter:  Specifcally, the color sequence X33020 (where X = any number) was searched for.  When found, the read was trimmed to remove the X33020 colors and anything after it.  Only reads with sizes of 20-24nts were retained.  Redundantly sequenced reads were collapsed and the trimmed colorspace reads were directly translated to DNA space.  The resulting processed fasta file indicates the number of reads in the header as follows: ">Pp_NOTAP_20-24_2_9" ..this read was found nine times (final field in header)

organism: Physcomitrium patens

source_name: protonemata

growth_protocol: Plants were grown on BCD media supplemented with ammonium tartarate in a 22C growth chamber with 16hrs light, 8 hrs. dark

extract_protocol: Total RNA was extracted using Tri-Reagent.  Small RNAs were fractionated by the use of the Ambion Flash Page system.  Barcoded small RNA libraries were prepared using the Ambion / ABI SOLiD Small RNA sequencing kit, per the manufacturer's instructions

value: Ppdcl4 knockout mutant

tag: tissue

value: protonemata

tag: barcode


title: Protonemata WT

value: wild-type


title: SINV-NoVB2

description: 18-30nt small RNA

data_processing:
small RNAs were mapped to the Ae. aegypti genome using Bowtie allowing for a single mismatch.
Genome Build:
dsSINV-NoVB2_unique_mapping_raw_reads.txt: AaegL1.2, September 2009

value: 4 days post injection

tag: presence of the novb2 protein

value: yes


title: 692NT

status: Public on Mar 31 2012

city: Bronx

first: Miao

last: Shi

state: NY

address: 1301 Morris Park Ave

department: Pulmonary Medicine

institute: Albert Einstein College of Medicine

description:
692NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.

data_processing: The microRNA analytical pipeline identifies microRNA sequences through adaptor removal, genomic alignment, and comparison with the miRBase database. The algorithm works as follows. First, the 3' Illumina adaptor is stripped off. Then, sequences ranging from 17 - 27 bases (the size of mature microRNAs) are aligned to genomic and RefSeq libraries (hg19) using Bowtie. Sequences that align to annotated regions of the genome are compared with known microRNAs in miRBase 16. A hit is defined as an aligned sequence that overlaps at least 50% with coordinates of a miRBase-defined microRNA.

source_name: Lung tissue

extract_protocol:
Total RNA isolation from tissue samples; 50mg of snap frozen lung tissue was added to a tube containing 1 ml of ice cold trizol and homogenized until tissue was totally homogenized. After incubation for 5 min at room temperature, 0.2 ml of chloroform was added; tube was shaked vigorously by hand for 15 sec and then incubated for 3 min at room temperature. Then samples were centrifuged for 20 min at 12000g at 4C. Aqueous phase was transfered to a clean 1.5-ml tube and 0.5 ml of isopropyl alcohol was added into the aqueous phase. Incubate the samples at room temperature for 10 min and centrifuge for 20 min at 12000g at 4C. Remove the supernatant and wash the RNA pellet with 75% ethanol. Air-dry the pellet and dissolve it in 20 ul of RNase-free water. Use nanodrop to measure RNA concentration and use agilent 2100 bioanalyzer to check RNA quality.
Libraries were prepared according to Illumina's instructions accompanying Small RNA Sample Prep Kit (CAT#:FC-102-1009).Briefly, ligate 3' RNA adapter to 3'-end of small RNA and ligate 3' RNA adapter to 3'-end of small RNA. Then perform RT-PCR amplification and gel-purify the small RNA library.

tag: tissue (t=tumor, nt=non-tumor)

value: NT

tag: phenotype (sq=squamous lung cancer, ad=adenocarcinoma lung cancer)

value: benign


title: 688NT

description:
688NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 675T

description:
675T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.

value: T

value: Ad


title: 692T

description:
692T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 670NT

description:
670NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 653NT

description:
653NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: SINV

description: 18-30nt small RNA

data_processing:
small RNAs were mapped to the Ae. aegypti genome using Bowtie allowing for a single mismatch.
Genome Build:
dsSINV_unique_mapping_raw_reads.txt: AaegL1.2, September 2009


title: 653T

description:
653T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 688T

description:
688T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 642NT

description:
642NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 670T

description:
670T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.

value: AdSq


title: 675NT

description:
675NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 642T

description:
642T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 551NT

description:
551NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 611T

description:
611T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.

value: Sq


title: 604NT

description:
604NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 551T

description:
551T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 618T

description:
618T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 618NT

description:
618NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 619T

description:
619T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 619NT

description:
619NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 542T

description:
542T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 610NT

description:
610NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 610T

description:
610T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 607T

description:
607T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 607NT

description:
607NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 606T

description:
606T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 606NT

description:
606NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 603NT

description:
603NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 603T

description:
603T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 560NT

description:
560NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 558NT

description:
558NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 539NT

description:
539NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 543T

description:
543T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 539T

description:
539T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 560T

description:
560T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 538T

description:
538T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 538NT

description:
538NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 534T

description:
534T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 542NT

description:
542NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 507T

description:
507T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 507NT

description:
507NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 596NT

description:
596NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 566T

description:
566T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 566NT

description:
566NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 596T

description:
596T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.