title: Mammary carcinoma, #13

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

description:
19_RF_MT
Gene expression in mammary carcinoma.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028279_D_F_20120224). Signal intensity data were normalized using Lowess normalization. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mammary carcinoma induced by radiation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the AllPrep DNA/RNA Mini kit (QIAGEN) following the manufacturer's recommendations.

tag: strain/background

value: F1 hybrid of Sprague-Dawley and Copenhagen

value: Mammary carcinoma

value: Female


title: SpColCtrl_305

status: Public on Feb 14 2018

type: SRA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

organism: Mus musculus

source_name: spleen

growth_protocol: Live cells were sorted by flow cytometry from the spleen and colon lamina propria of mice (carrying a Foxp3 reporter gene).

extract_protocol:
Spleen were mechanically dissociated and colon were digested with collagenase/dispase to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ GFP+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: tissue

value: spleen

tag: library name

tag: sample type

tag: strain

value: B6 Foxp3-Ires-Gfp

tag: Sex

value: male

tag: age (months)

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: Caprine Endometrial Epithelial Cells PPRV1h 1

type: RNA

city: Yangling

first: Bo

last: Yang

address: 22 Xinong Rd, College of Veterinary Medicine 4316

department: College of Veterinary Medicine,

country: China

institute: Northwest A&F University

description: Gene expression infection of PPRV

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 019921_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Capra hircus

source_name: EECs  PPRV 1h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Each group of samples was added by 1ml RNAiso Plus(TAKARA).RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Sheep Genome Oligo Microarray (8x15K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

treatment_protocol: PPRV with multiplicity of infection (MOI) of 2 was absorbed into the cells at 4 °C for 1 h. After fully adsorption, the cells were allowed to proceed at 37 °C for 1h. To determine the rate of virus internalization, a parallel set of cultures was processed under the same conditions, except that PPRV was replaced by culture medium.

tag: cell type

value: endometrial epithelial cells

tag: infection duration


title: Mammary carcinoma, #12

country: Japan

description:
18_RE_MT
Gene expression in mammary carcinoma.

organism: Rattus norvegicus

growth_protocol: Rats were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (CE-2; Clea Japan, Tokyo, Japan) and sterilized water ad libitum.

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (4 Gy, 0.5 Gy/min) at 7 weeks of age.

tag: gender


title: SpColCtrl_303


title: SpColCtrl_302


title: SpColCtrl_301


title: SpColCtrl_300


title: SpColCtrl_299


title: SpColCtrl_298


title: SpColCtrl_297


title: C. elegans fed HK E. coli, biological rep3

first: Grace

middle: J.

last: Yuen

state: Massachusetts

address: 185 Cambridge Street, CPZN-7724, Simches Research Building

department: Molecular Biology

institute: Massachusetts General Hospital

description: Young adult C. elegans fed heat-killed E. coli for 8 hours

hyb_protocol: Following fragmentation, cRNA were hybridized in the Hybridization Oven 640 for 16 hr at 45C onto the GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA and quantile normalization.

label: biotin

organism: Caenorhabditis elegans

source_name: Young adult fed heat-killed E. coli

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C. elegans were maintained on nematode growth media (NGM) and fed E. coli strain OP50.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Late L4-staged C. elegans worms washed 3x in excess M9W buffer and transferred to BHI medium-grown E. faecalis, B. subtilis, or heat-killed E. coli. The plates were then incubated at 25°C for 8 hours, after which they became young adults.

value: whole organism

tag: genotype

value: N2 (Bristol strain)

tag: age

value: Young adult

tag: treatment

value: fed heat-killed E. coli for 8 hours


title: Mammary carcinoma, #11

description:
17_RD_MT
Gene expression in mammary carcinoma.


title: C. elegans infected with E. faecium, biological rep3

description: Young adult C. elegans infected with E. faecium for 8 hours

source_name: Young adult infected with E. faecium

value: infected with E. faecium for 8 hours


title: Mammary carcinoma, #10

description:
16_R19_MT
Gene expression in mammary carcinoma.


title: Mammary carcinoma, #8

description:
14_R16_MT
Gene expression in mammary carcinoma.


title: SpColCtrl_296


title: C. elegans infected with E. faecium, biological rep2


title: Mammary carcinoma, #7

description:
13_R14_MT
Gene expression in mammary carcinoma.


title: C. elegans infected with E. faecalis, biological rep3

description: Young adult C. elegans infected with E. faecalis for 8 hours

source_name: Young adult infected with E. faecalis

value: infected with E. faecalis for 8 hours


title: C. elegans fed HK E. coli, biological rep4


title: dkfz_NCH3602_PDX

type: genomic

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: ETMR PDX

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

value: orthotopic PDX, passage 0


title: Mammary carcinoma, #9

description:
15_R17_MT
Gene expression in mammary carcinoma.


title: SpColCtrl_295


title: C. elegans infected with E. faecium, biological rep1


title: C. elegans infected with E. faecalis, biological rep2


title: Mammary carcinoma, #4

description:
10_R8_MT
Gene expression in mammary carcinoma.


title: Mammary carcinoma, #5

description:
11_R10_MT
Gene expression in mammary carcinoma.


title: C. elegans infected with E. faecalis, biological rep1


title: dkfz_NCH3602_tumor

source_name: ETMR tumor

value: primary tumor to ETMR PDX NCH3602


title: dkfz_BT183_tumor

value: primary tumor to ETMR cell line BT183


title: SpColCtrl_292


title: SpColCtrl_290


title: Mammary carcinoma, #6

description:
12_R12_MT
Gene expression in mammary carcinoma.


title: C. elegans fed B. subtilis, biological rep3

description: Young adult C. elegans fed B. subtilis for 8 hours

source_name: Young adult fed B. subtilis

value: fed B. subtilis for 8 hours


title: SpColCtrl_289


title: SpColCtrl_294


title: SpColCtrl_288


title: Mammary carcinoma, #2

description:
08_R4_MT
Gene expression in mammary carcinoma.

value: F1 hybrid of Sprague-Dawley and Copenhagen


title: C. elegans fed B. subtilis, biological rep2


title: SpColCtrl_287


title: C. elegans fed B. subtilis, biological rep1


title: Mammary carcinoma, #1

description:
07_R2_MT
Gene expression in mammary carcinoma.

value: Mammary carcinoma


title: C. elegans fed HK E. coli, biological rep2


title: SpColCtrl_286


title: SpColCtrl_285


title: Normal mammary gland, #1

description:
01_R3_MG
Gene expression in normal mammary gland.

source_name: Normal mammary gland

value: Normal mammary gland

value: Female


title: AS11-24027

city: San Francisco

first: Priscilla

last: Hsue

state: CA

address: 1001 Potrero Ave, Room 5G4

department: Medicine

institute: University of California, San Francisco

description:
HIV-
miRNA
SAMPLE 92

data_processing:
The non-normalized data (cycle threshold (Ct) values) were generated using the Fluidigm real-time qPCR analysis software. The parameters used were: 1) The threshold for determination of Ct values was set at the same value for all miRNA assays using the Auto Global setting. 2) The baseline was determined for all assays using the Linear Derivative setting.  The normalized data (available in sample table) are presented as log base 2 global mean-normalized relative expression values and were generated from the non-normalized Ct values through through a sequential process in the R statistical environment consisting of data filtering, global mean normalization within a sample, replacement of non-amplified reactions with a lower limit of detection based upon the lowest observed expression within a miRNA assay, and ending with scaling of the data through a subtraction such that the lowest expression value within a miRNA is zero. The scaling does not affect any downstream statistics or fold change calculations because the values are in a log base 2 relative expression scale. The initial filtering consisted of: 1) Ct values greater than 27 were converted to failed reactions to reduce noise. 2) Samples that did not amplify for at least 80% of the miRNA assays were removed; only one sample had to be removed for this reason. 3) miRNA assays that did not amplify for at least 80% of the samples were removed; as a result of this filter, 98 miRNA assays were removed with 94 miRNA assays remaining for statistical analysis. As we filtered miRNA assays and samples for adequate quality, we took undetectable amplification to represent non-expression rather than technical error in the PCR reaction. Of the 94 miRNA assays analyzed, two (miR-184 and miR-206) were duplicate assays and two (miR-1274a and miR-1274b) are no longer considered to be miRNAs. The duplicate assays are denoted by the addition of -1 to the name.  Fold Change was computed as 2^(log base 2 fold change), in which the log base 2 fold change of Group A relative to Group B was calculated in the R statistical environment as: the arithmetic mean of the log base 2 global mean-normalized relative expression values for Group B subjects minus the arithmetic mean of the log base 2 global mean-normalized relative expression values for Group A subjects.
In the Matrix normalized sheet, log base 2 global mean-normalized relative expression values, scaled to have a minimum value of zero within each miRNA assay, were computed in the R statistical environment as described above.  In the Fold Change sheet, the fold change of HIVPos/HIVNeg, and HIVElite/HIVNeg was computed in the R statistical environment from the log base 2 global mean-normalized relative expression values as described above.

source_name: plasma

label_protocol: Isolated RNA samples were converted to complementary DNA (cDNA) using TaqMan miRNA Reverse Transcription Kit and MegaPlex Human RT Primer Pool Av2.1 and Pool Bv3.0. (Life Technologies, Foster City, CA) in a 384 well Thermal Cycler. The cDNA samples were PreAmplified using TaqMan PreAmp Master Mix and PreAmp Primers, Human Pool A v2.1 and Pool B v3.0 (Life Technologies, Foster City, CA).

extract_protocol: Total RNA isolated from plasma samples using Rneasy Mini Kits (Qiagen) and an automated purification instrument, QIAcube (Qiagen)

value: plasma

value: Male

tag: race

value: White

tag: hiv duration (years hiv+)

value: Uninfected

tag: hypertension

value: No

tag: diabetes


title: Mammary carcinoma, #3

description:
09_R6_MT
Gene expression in mammary carcinoma.

tag: strain/background

tag: tissue


title: Normal mammary gland, #5

description:
05_R13_MG
Gene expression in normal mammary gland.


title: Normal mammary gland, #6

description:
06_RG_MG
Gene expression in normal mammary gland.


title: AS11-22907

description:
HIV+
miRNA
SAMPLE 91

value: African American


title: Normal mammary gland, #4

description:
04_R11_MG
Gene expression in normal mammary gland.


title: Normal external auditory canal epithelium_fresh tissues_rep6

city: Shanghai

first: Hong

last: Liu

state: Shanghai

address: 83 Fenyang Road

department: Department of Otology and Skull Base Surgery

institute: Eye & Ear Nose and Throat Hospital, Fudan University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 640 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded by Genesrping software (version 13.0; Agilent Technologies) and Transcriptome Analysis Console (version2.0, Affymetrix) separately.

label_protocol: Total RNA were amplified, labeled and purified by using WT Terminal Labeling and Controls Kit (Cat#901524, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Patients with external auditory canal squamous cell carcinoma (EACC) were collected successively who received surgery from June 2015 to March 2016 in the Eye Ear Nose and Throat Hospital, Fudan University. One pair of samples was collected from surgical specimen of each patient, including EACC and normal external auditory canal tissues. ESCC was confirmed by pathological examination.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: Patients did not received chemotherapy, radiotherapy or biological therapy before surgery. The normal external auditory canal tissues at a distance of more than 2 cm from tumor margin. Light microscope examination revealed that normal external auditory canal tissues were free of metaplasia, degeneration and inflammation. Selected tissues were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: Sex

value: female

tag: laterality of tumor

value: left

tag: tnm stage of tumor

tag: tumor defferentiation grade

value: I

value: Normal external auditory canal tissue collected from patients during surgery


title: Normal external auditory canal epithelium_fresh tissues_rep8

description: Light microscope examination revealed that normal external auditory canal tissues were free of metaplasia, degeneration and inflammation

value: male

value: right


title: C. elegans fed HK E. coli, biological rep1

description: Young adult C. elegans fed heat-killed E. coli for 8 hours

value: whole organism

value: N2 (Bristol strain)

value: Young adult

value: fed heat-killed E. coli for 8 hours


title: Normal mammary gland, #2

description:
02_R5_MG
Gene expression in normal mammary gland.

value: F1 hybrid of Sprague-Dawley and Copenhagen

value: Normal mammary gland

value: Female


title: SpColCtrl_284

value: spleen

tag: library name

tag: sample type

tag: strain

value: B6 Foxp3-Ires-Gfp

tag: age (months)

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: AS11-19846

description:
HIV-
miRNA
SAMPLE 90

value: plasma

tag: gender

value: Male

tag: race

value: Uninfected

value: No


title: Normal external auditory canal epithelium_fresh tissues_rep7

value: female

tag: age

value: I


title: AS11-18666

description:
HIV+
miRNA
SAMPLE 89

value: White

tag: hiv duration (years hiv+)

tag: hypertension

tag: diabetes


title: Normal mammary gland, #3

description:
03_R7_MG
Gene expression in normal mammary gland.

tag: strain/background

tag: tissue


title: SpColCtrl_283

tag: Sex

value: male


title: AS11-18505

description:
HIV+ Elite
miRNA
SAMPLE 88


title: AS11-16967

description:
HIV+ Elite
miRNA
SAMPLE 87


title: AS11-16958

description:
HIV+ Elite
miRNA
SAMPLE 86


title: SpColCtrl_280


title: Normal external auditory canal epithelium_fresh tissues_rep4

tag: laterality of tumor

value: right

tag: tnm stage of tumor

tag: tumor defferentiation grade

value: Normal external auditory canal tissue collected from patients during surgery


title: AS11-14318

description:
HIV+ Elite
miRNA
SAMPLE 85

value: African American


title: Normal external auditory canal epithelium_fresh tissues_rep5


title: SpColCtrl_278

tag: library name

tag: sample type

tag: strain


title: Normal external auditory canal epithelium_fresh tissues_rep3

value: left

value: II


title: SpColCtrl_279

tag: age (months)

tag: total number of reads

tag: number of mapped reads


title: SpColCtrl_276

tag: number of unique reads (umi)


title: Normal external auditory canal epithelium_fresh tissues_rep2

tag: age


title: AS11-13433

description:
HIV+
miRNA
SAMPLE 84

tag: gender

tag: race

tag: hiv duration (years hiv+)


title: AS11-10795

description:
HIV+
miRNA
SAMPLE 82

tag: hypertension

tag: diabetes


title: External auditory canal squamous cell carcinoma_fresh tissue_rep7

description: External auditory canal squamous cell carcinoma was confirmed by histopathological diagnosis

tag: Sex

tag: tissue

value: External auditory canal squamous cell carcinoma tissue collected from patients during surgery


title: AS11-12758

description:
HIV+
miRNA
SAMPLE 83

value: Latino


title: 106405188_T

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

hyb_protocol: Illumina Infinium protocol

scan_protocol: iScan

data_processing: Genotyping module (v.1.9.4) in GenomeStudio v.2011.1 (Illumina) to calculate B-allele frequencies (BAF) and logR ratios.

source_name: Colon

label_protocol: Illumina Infinium protocol

extract_protocol: Qiagen Allprep Kit

tag: cell type

value: Primary tumour

value: Colon

tag: sample_id_in the manuscript


title: 106698801_M

source_name: Liver

value: Metastasis

value: Liver


title: Normal external auditory canal epithelium_fresh tissues_rep1

tag: laterality of tumor

tag: tnm stage of tumor

tag: tumor defferentiation grade


title: 106405188_M


title: SpColCtrl_281

value: spleen

tag: library name

tag: sample type

tag: strain

value: B6 Foxp3-Ires-Gfp

tag: age (months)


title: 106366874_T


title: 106698801_T


title: AS11-10029

description:
HIV+ Elite
miRNA
SAMPLE 81

value: plasma

value: Male

value: No


title: 106366874_M


title: SpColCtrl_274

value: male

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: SpColCtrl_275


title: External auditory canal squamous cell carcinoma_fresh tissue_rep3

tag: age


title: 105641794_M


title: External auditory canal squamous cell carcinoma_fresh tissue_rep4

value: right

value: I


title: 105641794_T


title: AS11-09311

description:
HIV-
miRNA
SAMPLE 80

tag: gender

tag: race

value: Other

tag: hiv duration (years hiv+)

value: Uninfected

tag: hypertension


title: SpColCtrl_273

tag: tissue

tag: Sex


title: External auditory canal squamous cell carcinoma_fresh tissue_rep6

value: female

tag: laterality of tumor

value: left


title: External auditory canal squamous cell carcinoma_fresh tissue_rep5

tag: tnm stage of tumor

value: External auditory canal squamous cell carcinoma tissue collected from patients during surgery


title: External auditory canal squamous cell carcinoma_fresh tissue_rep2

tag: tumor defferentiation grade

value: II


title: AS11-09215

description:
HIV-
miRNA
SAMPLE 79

value: African American

value: Yes

tag: diabetes


title: SpColCtrl_272

tag: library name

tag: sample type


title: SpColCtrl_270

tag: strain

tag: age (months)


title: External auditory canal squamous cell carcinoma_fresh tissue_rep8


title: 105424267_T

tag: cell type

value: Primary tumour

value: Colon

tag: sample_id_in the manuscript


title: 105406405_T


title: 105406405_M

value: Metastasis

value: Liver


title: 105424267_M


title: AS11-06444

description:
HIV+
miRNA
SAMPLE 77

value: plasma

value: Male

value: White


title: SpColCtrl_268

value: spleen

value: B6 Foxp3-Ires-Gfp

value: male

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: SpColCtrl_267


title: 105311309_T


title: AS11-07947

description:
HIV+ Elite
miRNA
SAMPLE 78

tag: gender

tag: race

tag: hiv duration (years hiv+)

value: No


title: SpColCtrl_266

tag: tissue

tag: Sex


title: AS11-06243

description:
HIV+
miRNA
SAMPLE 76

tag: hypertension


title: AS11-05221

description:
HIV+ Elite
miRNA
SAMPLE 75


title: SpColCtrl_269


title: AS11-05140

description:
HIV+
miRNA
SAMPLE 74

value: Other


title: 105311309_M


title: SpColCtrl_265


title: AS11-04095

description:
HIV-
miRNA
SAMPLE 73

value: Uninfected


title: 105287255_M


title: 105287255_T


title: 105145928_T


title: AS11-03953

description:
HIV+
miRNA
SAMPLE 72


title: SpColCtrl_264


title: SpColCtrl_262


title: SpColCtrl_263


title: 105145928_M


title: AS11-03619

description:
HIV+ Elite
miRNA
SAMPLE 71


title: 104768788_T


title: SpColCtrl_261


title: SpColCtrl_260


title: SpColCtrl_259


title: External auditory canal squamous cell carcinoma_fresh tissue_rep1

value: female

tag: laterality of tumor

value: right

tag: age

tag: tnm stage of tumor

tag: tumor defferentiation grade

value: External auditory canal squamous cell carcinoma tissue collected from patients during surgery


title: AS11-02680

description:
HIV+
miRNA
SAMPLE 69

tag: diabetes


title: AS11-02832

description:
HIV+
miRNA
SAMPLE 70

value: African American


title: 104768788_M


title: SpColCtrl_258

tag: library name

tag: sample type

tag: strain

tag: age (months)


title: AS10-22477

description:
HIV+ Elite
miRNA
SAMPLE 67

value: Yes


title: 104356255_T

tag: cell type

value: Primary tumour

value: Colon

tag: sample_id_in the manuscript


title: 104356255_M

value: Metastasis

value: Liver


title: AS10-22073

description:
HIV+
miRNA
SAMPLE 66

value: plasma

tag: gender

value: Male


title: SpColCtrl_257

value: spleen

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: SpColCtrl_256

tag: tissue

value: B6 Foxp3-Ires-Gfp

tag: Sex


title: AS10-19205

description:
HIV+
miRNA
SAMPLE 65

tag: race

tag: hiv duration (years hiv+)

tag: hypertension


title: 103625327_T


title: AS10-18795

description:
HIV+
miRNA
SAMPLE 64


title: 103121614_T


title: AS11-01772

description:
HIV+ Elite
miRNA
SAMPLE 68

value: White


title: AS10-15037

description:
HIV-
miRNA
SAMPLE 62

value: No


title: 103625327_M


title: SpColCtrl_253

value: male


title: SpColCtrl_254


title: AS10-16689

description:
HIV-
miRNA
SAMPLE 63

value: Uninfected


title: 102680525_T


title: 103121614_M


title: 102680525_M


title: AS10-13815

description:
HIV+ Elite
miRNA
SAMPLE 59


title: TIME cells co-cultured with cancer associated fibroblasts, biological rep2

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from TIME cells co-cultured with cancer assocaited fibroblasts

hyb_protocol: cRNA samples were hybridized for 16 hr on Clariom D human arrays according to the manufacturer's instruction. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label: Biotin

label_protocol: Sample labeling were performed using the Clariom D Pico Assay (Thermo Fisher) with 2ng of total RNA as input according to the manufacturer's instruction.

growth_protocol: Ovarian fibroblasts was cultured with medium M105/199 supplemented with 10% Fetal bovine serum and 1ng/mL Epidermal growth factor. TIME cells were cultured in endothelial cell growth medium-2 (Lonza). All cell types were cultured in a humidified incubator at 37C with 5% carbon dioxide.

extract_protocol: Total RNA extraction was performed using the Purelink RNA mini kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: 1 x 10^4 TIME human MECs were co-cultured with either 2 x 10^4 primary ovarian CAFs or 2 x 10^4 normal ovarian fibroblasts (NFs) in Boyden chambers for 48 hours

tag: cell line

value: TIME


title: AS10-14206

description:
HIV+
miRNA
SAMPLE 60

value: Other

tag: diabetes


title: SpColCtrl_250

tag: library name


title: SpColCtrl_252

tag: sample type


title: SpColCtrl_291

tag: strain


title: TIME cells co-cultured with cancer associated fibroblasts, biological rep1


title: TIME cells co-cultured with normal fibroblasts, biological rep2

description: Gene expression data from TIME cells co-cultured with normal fibroblasts


title: SpColCtrl_249

tag: age (months)


title: SpColCtrl_248


title: SpColCtrl_255


title: 102222035_T

tag: cell type


title: 101836493_M

tag: sample_id_in the manuscript


title: 101836493_T


title: SpColCtrl_246


title: SpColCtrl_245


title: 102222035_M


title: AS10-10709

description:
HIV+
miRNA
SAMPLE 57

tag: gender


title: AS10-08851

description:
HIV+ Elite
miRNA
SAMPLE 56


title: AS10-13105

description:
HIV+
miRNA
SAMPLE 58


title: AS10-14749

description:
HIV+
miRNA
SAMPLE 61


title: AS10-08600

description:
HIV+
miRNA
SAMPLE 55

value: Latino


title: N3-1

first: Renyi

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 5 ). Clean reads were mapped to the lettuce (Lactuca sativa L.) genome sequence (http://lgr.genomecenter.ucdavis.edu)  using HISAT. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 CPM (counts per million) in at least two samples were kept for further analysis.
Genome_build: Lactuca sativa cv Salinas V5 (http://lgr.genomecenter.ucdavis.edu)
Supplementary_files_format_and_content: Tab-delimited text file include CPM (counts per Million) values for 16 Samples .

organism: Lactuca sativa

source_name: shoot apical meristem

growth_protocol: The lettuce line S39 and S24 are planted in the growth chamber at 25/15ºC (day/night), and using a 16 h day/8 h night with a photon flux density (PFD) of 200µmol photons m−2s−

extract_protocol:
Laser capture microdissection was used to collect shoot cells at four time-course stage of these two lines.Total RNA from LCM samples was extracted using the Arcturus PicoPure RNA isolation Kit (Applied Biosystems) in conjunction with DNase I (Qiagen) for removing potential DNA contamination. The Target Amp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (Epicentre Biotechnologies) was used for RNA amplification following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using Illumina HiSeq 2000

treatment_protocol: No treatment

tag: line

value: lettuce  line S24

tag: phenotype

value: bolting-resistant

tag: age

value: 45 days after planting


title: TIME cells co-cultured with normal fibroblasts, biological rep1


title: AS10-08456

description:
HIV-
miRNA
SAMPLE 54

tag: tissue


title: SpColCtrl_237

tag: Sex

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: N2-1

value: 35 days after planting


title: N2-2


title: SpColCtrl_236


title: N1-2

value: 28 days after planting


title: AS10-07208

description:
HIV+
miRNA
SAMPLE 52

tag: race

tag: hiv duration (years hiv+)

tag: hypertension


title: AS10-07513

description:
HIV+ Elite
miRNA
SAMPLE 53

tag: diabetes


title: N1-1


title: N0-2

value: 20 days after planting


title: N3-2


title: AS10-06624

description:
HIV+
miRNA
SAMPLE 51

value: plasma

value: African American

value: Yes


title: AS10-06548

description:
HIV+
miRNA
SAMPLE 50

value: Male


title: SpColCtrl_233

value: spleen

tag: library name

tag: sample type

tag: strain

value: B6 Foxp3-Ires-Gfp


title: N0-1


title: B3-2

value: lettuce  line S39

value: bolting-sensitive


title: AS10-04490

description:
HIV+
miRNA
SAMPLE 49

value: White

value: No


title: SpColCtrl_244

value: male

tag: age (months)


title: AS10-04322

description:
HIV+
miRNA
SAMPLE 48

tag: gender


title: SpColCtrl_231


title: SpColCtrl_229


title: AS10-01722

description:
HIV+
miRNA
SAMPLE 46


title: SpColCtrl_230


title: B3-1

tag: line


title: B2-1

tag: phenotype


title: SpColCtrl_226


title: SpColCtrl_228


title: B2-2

tag: age


title: AS10-04079

description:
HIV-
miRNA
SAMPLE 47

tag: tissue

value: Uninfected


title: SpColCtrl_234

tag: Sex


title: SpColCtrl_232

tag: total number of reads


title: SpColCtrl_225

tag: number of mapped reads


title: SpColCtrl_223

tag: number of unique reads (umi)


title: B1-2


title: AS10-00317

description:
HIV+
miRNA
SAMPLE 43

tag: race


title: AS10-008222

description:
HIV+
miRNA
SAMPLE 44

value: Other

tag: hiv duration (years hiv+)


title: SpColCtrl_224


title: B1-1


title: SpColCtrl_217


title: AS09-17198

description:
HIV+
miRNA
SAMPLE 41

tag: hypertension


title: SpColCtrl_221


title: AS09-17112

description:
HIV+
miRNA
SAMPLE 40

tag: diabetes


title: AS09-16092

description:
HIV+ Elite
miRNA
SAMPLE 39


title: SpColCtrl_214

tag: library name


title: AS09-15934

description:
HIV+
miRNA
SAMPLE 37


title: SpColCtrl_213

tag: sample type


title: AS10-01596

description:
HIV+
miRNA
SAMPLE 45


title: SpColCtrl_212

tag: strain


title: SpColCtrl_211

tag: age (months)


title: AS09-14211

description:
HIV+
miRNA
SAMPLE 35

tag: gender

value: Latino


title: AS09-14148

description:
HIV+
miRNA
SAMPLE 34


title: B0-2

tag: line


title: AS09-14063

description:
HIV+
miRNA
SAMPLE 33


title: B0-1

tag: phenotype


title: SpColCtrl_208


title: AS09-17446

description:
HIV+
miRNA
SAMPLE 42


title: SpColCtrl_207


title: AS09-13590

description:
HIV+
miRNA
SAMPLE 32


title: SpColCtrl_216


title: AS09-12514

description:
HIV-
miRNA
SAMPLE 31


title: AS09-15949

description:
HIV+
miRNA
SAMPLE 38

value: Female


title: AS09-06737

description:
HIV+
miRNA
SAMPLE 30


title: AS09-05990

description:
HIV+
miRNA
SAMPLE 28


title: AS09-06607

description:
HIV+
miRNA
SAMPLE 29


title: SpColCtrl_215


title: AS09-04726

description:
HIV+ Elite
miRNA
SAMPLE 26


title: AS09-04551

description:
HIV-
miRNA
SAMPLE 25


title: AS09-05478

description:
HIV-
miRNA
SAMPLE 27


title: AS09-14580

description:
HIV+ Elite
miRNA
SAMPLE 36


title: AS09-04360

description:
HIV+
miRNA
SAMPLE 24


title: delta ClpX Bacillus anthracis Sterne replicate 2

city: Fort Worth

first: Shauna

last: McGillivray

address: 2800 S. University Dr

department: Biology

institute: TCU

description:
This sample is of deltaClpX Bacillus anthracis Sterne. It is the second of three deltaClpx biological replicates used in this experiment, each from separate cultures.
dClpX2

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Bacillus anthracis str. Sterne

source_name: delta ClpX Bacillus anthracis Sterne

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Bacterial strains were grown to early log phase (O.D.600nm 0.4) aerobically at 37°C in Brain Heart Infusion media.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc). DNA was removed using the Turbo DNA-free kit following the rigorous protocol described in manufacturers instructions (Thermo Fisher Scientific). RNA was concentrated using the Zymo RNA Clean & Concentrator-5 kit (Zymo Research). RNA quality and concentration was determined on the AGilent Bioanalyzer and NanoDrop spectrophotometer.  All samples passed QC metrics set forth by Roche NimbleGen.

tag: genotype

value: deletion mutant deltaClpX


title: delta ClpX Bacillus anthracis Sterne replicate 3

description:
This sample is of deltaClpX Bacillus anthracis Sterne. It is the third of three deltaClpx biological replicates used in this experiment, each from separate cultures.
dClpX3


title: wild-type Bacillus anthracis Sterne replicate 2

description:
This sample is of wild-type Bacillus anthracis Sterne. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.
WT2

source_name: wild-type Bacillus anthracis Sterne

value: wild-type


title: AS09-04310

description:
HIV+ Elite
miRNA
SAMPLE 23

tag: tissue

value: plasma


title: wild-type Bacillus anthracis Sterne replicate 3

description:
This sample is of wild-type Bacillus anthracis Sterne. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.
WT3


title: delta ClpX Bacillus anthracis Sterne replicate 1

description:
This sample is of deltaClpX Bacillus anthracis Sterne. It is the first of three deltaClpx biological replicates used in this experiment, each from separate cultures.
dClpX1


title: AS09-03857

description:
HIV-
miRNA
SAMPLE 22


title: AS09-02649

description:
HIV+
miRNA
SAMPLE 21


title: AS09-01273

description:
HIV-
miRNA
SAMPLE 18


title: AS09-00914

description:
HIV-
miRNA
SAMPLE 17


title: AS09-02607

description:
HIV-
miRNA
SAMPLE 20


title: AS09-01992

description:
HIV-
miRNA
SAMPLE 19


title: AS08-16891

description:
HIV-
miRNA
SAMPLE 12


title: AS08-18894

description:
HIV+
miRNA
SAMPLE 16

value: African American


title: Sample 16: Muscle, essential oil supplement

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

data_processing:
The quality of raw sequences was checked using FastQC. The adapter removal and trimming were done with Trimmomatic v.0.33.
High quality reads were aligned using STAR v.2.4.0.1  to the sheep reference genome. HTSeq v.0.6.1  was used to count reads.
Genome_build: Ovis Aries 3.1
Supplementary_files_format_and_content: Tab separated files with ensemble gene names and read counts in each row

organism: Ovis aries

source_name: Muscle

extract_protocol:
At slaughtering, liver and muscle tissue samples were collected. Tissues were frozen in liquid nitrogen and stored at -80°C. RNA  was isolated using TRIzol Plus RNA Purification Kit .
RNA Sequencing libraries were prepared using the Illumina TruSeq2 kit, poly-A mRNA purification and 1 ug of total RNA. RNA libraries were prepared for sequencing using standard Illumina HiSeq 1500 platform generating 101 base-paired end reads.

treatment_protocol: Essential Oil diet vs Control diet.

value: Muscle

tag: age

value: 171 postnatal days

tag: diet

value: essential oil supplement


title: AS08-18076

description:
HIV+
miRNA
SAMPLE 13

value: Male


title: AS08-18342

description:
HIV-
miRNA
SAMPLE 14


title: AS08-18487

description:
HIV+ Elite
miRNA
SAMPLE 15


title: Sample 15: Muscle, essential oil supplement

value: 175 postnatal days


title: AS08-16694

description:
HIV-
miRNA
SAMPLE 11


title: Sample 14: Muscle, essential oil supplement

value: 173 postnatal days


title: Sample 13: Muscle, essential oil supplement

value: 169 postnatal days


title: wild-type Bacillus anthracis Sterne replicate 1

description:
This sample is of wild-type Bacillus anthracis Sterne. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.
WT1


title: AS08-15572

description:
HIV-
miRNA
SAMPLE 10

value: No


title: AS08-15171

description:
HIV-
miRNA
SAMPLE 8

value: White

value: Yes


title: AS08-14962

description:
HIV+
miRNA
SAMPLE 7


title: AS08-15347

description:
HIV-
miRNA
SAMPLE 9

value: Uninfected


title: Sample 11: Muscle, essential oil supplement

value: 190 postnatal days


title: Sample 10: Muscle, essential oil supplement

value: 165 postnatal days


title: OB_WT_18M_R3

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

hyb_protocol: Labeled sense cDNA was hybridized to the GeneChip® Mouse Clariom S Arrays, washed and stained on a GeneChip® Fluidics 450 workstation (Affymetrix) according to the manufacturer protocols.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000 7G

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: Olfactory bulb

label_protocol: The sense cDNA was prepared from 1 ng of total RNA using the Affymetrix GeneChip® WT Pico Kit (PN902623). The sense strand cDNA was then fragmented and biotinylated according to the manufacturer's instructions.

extract_protocol: For olfactory bulb mRNA extraction, the Maxwell 16 simplyRNA kit (Promega) was used

value: female

tag: genotype/variation

value: wild type

value: Olfactory bulb


title: OB_WT_18M_R2


title: Sample 9: Muscle, essential oil supplement

value: 167 postnatal days


title: AS08-12862

description:
HIV+
miRNA
SAMPLE 6

value: plasma


title: OB_WT_18M_R1


title: AS08-11140

description:
HIV+ Elite
miRNA
SAMPLE 5


title: Sample 8: Muscle, control diet

value: Muscle

value: 154 postnatal days

value: control diet


title: OB_TG2576_18M_R2

value: Tg2576 transgenic


title: AS08-09097

description:
HIV+
miRNA
SAMPLE 4

value: Male

value: Other


title: OB_TG2576_18M_R3


title: OB_TG2576_18M_R1


title: Sample 12: Muscle, essential oil supplement

value: 173 postnatal days

value: essential oil supplement


title: AS08-06322

description:
HIV+
miRNA
SAMPLE 3

value: White

value: No


title: Sample 7: Muscle, control diet

value: 186 postnatal days


title: Scramble_ 24h Mtb infected_ experiment3_ replicate1

city: Berlin

first: Fadhil

last: Ahsan

address: Cahriteplatz 1

department: Immunology

institute: Max Planck Institute for Infection Biology

hyb_protocol: Quantity and labeling efficiency were verified before hybridization of the samples to SurePrint G3 Mouse GE 8x60K Microarray (Agilent Technologies, Product Number G4852A, Design ID 028005) according to manufacturer's instruction

scan_protocol: Scanning of microarrays was performed with 3μm resolution using a high-resolution laser microarray scanner (Agilent Technologies G2565CA)

data_processing: Data analysis was performed in R version 3.2.3 (2015-12-10), and a script including all analysis steps is available upon request. The data sets have been analyzed with limma R package for differential expression analysis (Ritchie et al., 2015). The data sets were background corrected using the normexp method and quantile normalized. Limma lmFit function was used to fit linear models which included factors: stimulus type (TB, control) and time point. The p-values were calculated based on the moderated t-statistic and most differentially regulated genes were retrieved with topTable function

source_name: experiment3, Scramble, 24h Mtb infected

label_protocol: RNA was labeled with the Low Input Quick Amp Labeling (Agilent Technologies) according to manufacturer’s instructions

growth_protocol: THP-1 monocytes (ATCC: TIB-202) were differentiated into macrophages using 100 nM PMA for 48 hours in complemented RPMI

extract_protocol: Trizol extraction protocol (Invitrogen) was used according to the manufacturer's instructions. The RNA yield and A260/280 ratio were measured with a NanoDrop ND 100 spectrometer (NanoDrop Technologies), and RNA integrity was verified using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Complemented RPMI without antibiotics serves as negative control. Mycobacterium tuberculosis strain H37Rv (ATCC : 27294) is used for infection

tag: cell type

value: THP-1 macrophage

tag: shRNA

value: scramble

tag: agent

value: Mycobacterium tuberculosis


title: Scramble_ 0h uninfected_ experiment3_ replicate2

source_name: experiment3, Scramble, 0h uninfected

value: uninfected


title: YQ2 + FBS 24h_rep3

city: San Michele all'Adige

first: Lisa

last: Rizzetto

address: via E. Mach 1

department: Research and Innovation Centre

country: Italy

institute: Fondazione Edmund Mach

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-065138 8x15k C. albicans assembly 21 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8X15k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (Grid: 065138_D_F_20140313 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Candida albicans

source_name: C. albicans YQ2, RPMI w/ 10% FBS, 24h, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-8000 Spectrophotometer.

extract_protocol: RNA was isolated at 1 h and 24 h from collected cells by the hot acid phenol extraction protocol.

treatment_protocol: C. albicans YL1 and YQ2 strains have been plated at a concentration of 1x107 cell/ml in complete RPMI in presence or absence of 10% FBS for 1 or 24 hr.

tag: development stage

value: cells

tag: treatment

value: with 10% FBS

tag: timepoint


title: IL36R knockdown_ 24h Mtb infected_ experiment3_ replicate1

source_name: experiment3, IL36R knockdown, 24h Mtb infected


title: Scramble_ 24h Mtb infected_ experiment3_ replicate2


title: IL36R knockdown_ 24h Mtb infected_ experiment3_ replicate2


title: IL36R knockdown_ 0h uninfected_ experiment3_ replicate1

source_name: experiment3, IL36R knockdown, 0h uninfected


title: IL36R knockdown_ 0h uninfected_ experiment3_ replicate2


title: AS08-02228

description:
HIV+
miRNA
SAMPLE 2

value: plasma

tag: race

tag: hiv duration (years hiv+)

tag: hypertension

tag: diabetes


title: Sample 3: Muscle, control diet

value: Muscle

value: 190 postnatal days


title: Scramble_ 0h uninfected_ experiment3_ replicate1


title: Sample 2: Muscle, control diet

value: 170 postnatal days

value: control diet


title: Sample 6: Muscle, control diet

value: 189 postnatal days


title: Sample 5: Muscle, control diet


title: Sample 16: Liver, essential oil supplement

value: Liver

value: 171 postnatal days


title: AS08-02006

description:
HIV+
miRNA
SAMPLE 1

tag: gender

value: Male

value: Other

value: Yes


title: YL1 - FBS 24h_rep3

source_name: C. albicans YL1, RPMI wo/ 10% FBS, 24h, replicate 1

tag: strain

value: no 10% FBS


title: YL1 + FBS 24h_rep3

source_name: C. albicans YL1, RPMI w/ 10% FBS, 24h, replicate 1


title: YQ2 + FBS 1h_rep3

source_name: C. albicans YQ2, RPMI w/ 10% FBS, 1h, replicate 1


title: YQ2 - FBS 1h_rep3

source_name: C. albicans YQ2, RPMI w/o 10% FBS, 1h, replicate 1


title: Sample 1: Muscle, control diet


title: YQ2 - FBS 24h_rep3

source_name: C. albicans YQ2, RPMI w/o 10% FBS, 24h, replicate 1


title: IL1R1 knockdown_ 24h Mtb infected_ experiment3_ replicate1

source_name: experiment3, IL1R1 knockdown, 24h Mtb infected

value: THP-1 macrophage


title: IL1R1 knockdown_ 0h uninfected_ experiment3_ replicate1

source_name: experiment3, IL1R1 knockdown, 0h uninfected


title: Ctrl for 5azaC-treated H1299, bio rep-2

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description: untreated H1299

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Affymetrix Expression Console Software (version 1.4) which normalizes array signals using  Signal Space Transformation (SST) and  robust multiarray averaging (RMA) algorithm.
probe group file: Clariom_S_Human.r1.pgf
meta-probeset file: Clariom_S_Human.r1.mps

source_name: Lung cell line H1299, untreated

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were maintained in RPMI1640 medium supplemented with 10% FBS, penicillin (100 U/mL) and streptomycin (100 μg/mL). Cells were maintained at 37°C in a humidified 5% CO2 incubator

extract_protocol: Total RNA were extracted from cultured cells using RNeasy Mini-kit (Qiagen, MD, USA) followed the manufacturer’s protocol as described previously.

treatment_protocol: Cells were treated with either 10 mM of GA or 5azaC for 120 h. Untreated cells of the same passage were used as controls.

value: lung

tag: cell line

tag: tumor type

value: non-small cell lung carcinoma

value: untreated


title: IL1R1 knockdown_ 0h uninfected_ experiment3_ replicate2

value: uninfected


title: TIME cells co-cultured with cancer associated fibroblasts, biological rep3

value: TIME


title: IL1R1 knockdown_ 24h Mtb infected_ experiment3_ replicate2

value: Mycobacterium tuberculosis


title: Sample 15: Liver, essential oil supplement

source_name: Liver

tag: tissue

tag: age

value: 175 postnatal days

value: essential oil supplement


title: YL1 + FBS 1h_rep3

source_name: C. albicans YL1, RPMI w/ 10% FBS, 1h, replicate 1

value: cells

value: with 10% FBS


title: Ctrl for 5azaC-treated H1299, bio rep-1

description: untreated H1299


title: YL1 - FBS 1h_rep3

source_name: C. albicans YL1, RPMI w/o 10% FBS, 1h, replicate 1


title: 5azaC-treated H1299, bio rep-2

description: H1299 cell line treated with 5azaC for 120 h

source_name: Lung cell line H1299, 5azaC treated, 120 h

value: 5azaC treated, 120 h


title: 5azaC-treated H1299, bio rep-1


title: Scramble_ 24h Mtb infected_ experiment2_ replicate2

source_name: experiment2, Scramble, 24h Mtb infected

value: scramble


title: Ctrl for GA-treated H1299, bio rep-2

description: untreated H1299


title: Scramble_ 0h uninfected_ experiment2_ replicate1

source_name: experiment2, Scramble, 0h uninfected


title: Ctrl for GA-treated H1299, bio rep-1

description: untreated H1299


title: Sample 14: Liver, essential oil supplement

value: Liver

value: 173 postnatal days

tag: diet


title: Sample 13: Liver, essential oil supplement

value: 169 postnatal days


title: Sample 12: Liver, essential oil supplement


title: Scramble_ 24h Mtb infected_ experiment2_ replicate1

tag: cell type


title: GA-treated H1299, bio rep-2

description: H1299 cell line treated with GA for 120 h

source_name: Lung cell line H1299, GA treated, 120 h

value: GA treated, 120 h


title: YQ2 + FBS 24h_rep2

source_name: C. albicans YQ2, RPMI w/ 10% FBS, 24h, replicate 1


title: Sample 11: Liver, essential oil supplement

value: 190 postnatal days


title: Sample 10: Liver, essential oil supplement

value: 165 postnatal days


title: YQ2 - FBS 24h_rep2

value: no 10% FBS


title: Sample 8: Liver, control diet

value: 154 postnatal days

value: control diet


title: YL1 - FBS 24h_rep2

source_name: C. albicans YL1, RPMI w/o 10% FBS, 24h, replicate 1


title: Sample 6: Liver, control diet

value: 189 postnatal days


title: YL1 + FBS 24h_rep2


title: IL36R knockdown_ 0h uninfected_ experiment2_ replicate2

source_name: experiment2, IL36R knockdown, 0h uninfected

value: THP-1 macrophage

tag: shRNA

value: uninfected


title: YQ2 + FBS 1h_rep2


title: Scramble_ TB24h Mtb infected_ experiment 1_ replicate1

source_name: experiment1, Scramble, TB24h Mtb infected

tag: agent

value: Mycobacterium tuberculosis


title: IL36R knockdown_ TB24h Mtb infected_ experiment2_ replicate1

source_name: experiment2, IL36R knockdown, TB24h Mtb infected


title: Sample 7: Liver, control diet

value: 186 postnatal days


title: GA-treated H1299,bio rep-1

value: lung

value: non-small cell lung carcinoma


title: YQ2 - FBS 1h_rep2

source_name: C. albicans YQ2, RPMI w/o 10% FBS, 1h, replicate 1

tag: development stage

value: cells


title: Sample 9: Liver, essential oil supplement

value: Liver

value: 167 postnatal days

value: essential oil supplement


title: YL1 - FBS 1h_rep2

tag: treatment


title: YL1 + FBS 1h_rep2

value: with 10% FBS

tag: timepoint


title: YQ2 - FBS 24h_rep1

source_name: C. albicans YQ2, RPMI w/o 10% FBS, 24h, replicate 1


title: Sample 5: Liver, control diet

value: 190 postnatal days


title: Scramble_ 0h uninfected_ experiment 1_ replicate1

source_name: experiment1, Scramble, 0h uninfected

value: scramble


title: Scramble_ 0h uninfected_ experiment 1_ replicate2


title: YQ2 + FBS 24h_rep1


title: IL36R knockdown_ 24h Mtb infected_ experiment 1_ replicate1

source_name: experiment1, IL36R knockdown, 24h Mtb infected


title: Sample 4: Liver, control diet

value: 173 postnatal days


title: YL1 - FBS 24h_rep1

value: no 10% FBS


title: IL36R knockdown_ 0h uninfected_ experiment2_ replicate1


title: IL36R knockdown_ 0h uninfected_ experiment 1_ replicate1

source_name: experiment1, IL36R knockdown, 0h uninfected


title: IL1R1 knockdown_ 24h Mtb infected_ experiment 1_ replicate2

source_name: experiment1, IL1R1 knockdown, 24h Mtb infected


title: Ago-1 Over expressed Eye Tm-8 TR1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: microRNA expression in fly eye

hyb_protocol: The samples were hybridized on the Drosophila miRNA 8x15K Arrays. The hybridization was carried out at 55°C for 20 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes.

scan_protocol: The microarray slide was scanned on a G2600D scanner (Agilent Technologies).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Drosophila melanogaster

source_name: Freshly (1d) emarged fly eye of UAS Ago-1/GMR GAL4

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Part Number: 5190-0456). The total RNA sample was diluted to 100ng/ul in nuclease free water and 200ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master mix (Agilent Technologies, Part Number: 5190-0456) by incubating at 37oC for 30 minutes. The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide and heating at 100 oC for 10 minutes and transferred to ice-water bath. The Ligation master mix (Agilent Technologies, Part Number: 5190-0456) containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16oC for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus, Catalog Number 5305000) at 45oC for 2 hour. The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking solution (Agilent Technologies, Part Number: 5190-0456) and Hi-RPM Hybridization Buffer (Agilent Technologies, Part Number: 5190-0456) and incubated at 100oC for 5 minutes followed by snap chill on ice for 5 minutes.

growth_protocol: Flies were grown at 24°C temperature with yeast-agar-cornmeal standard medium.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions and concentrations were determined using a NanoDrop-1000 spectrophotometer at absorbance of 260 nm. RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No Treatment

value: Head region (contains mainly adult Eye part)

tag: genotype/variation

value: Ago-1 overexpressed (UAS Ago-1/GMR GAL4)


title: Ago-1 Heteroallelic Mutant Eye Tm-6 TR1

description: microRNA expression in fly eye

source_name: Freshly (1d) emarged eye of Ago-1 hetero allelic mutant Fly

value: Ago-1 mutant (Ago-1^72/ Ago-1^45)


title: Ago-1 Heteroallelic Mutant Eye Tm-6 TR2

description: microRNA expression in fly eye


title: Ago-1 Over expressed Eye Tm-8 TR2

description: microRNA expression in fly eye


title: Sample 3: Liver, control diet

source_name: Liver

value: control diet


title: Sample 1: Liver, control diet

value: 171 postnatal days


title: Scramble_ 0h uninfected_ experiment2_ replicate2

value: THP-1 macrophage

value: uninfected


title: Sample 2: Liver, control diet

value: 170 postnatal days


title: YL1 + FBS 24h_rep1

source_name: C. albicans YL1, RPMI w/ 10% FBS, 24h, replicate 1

value: cells


title: GMR Eye Tm-5 TR2

description: microRNA expression in fly eye

source_name: Freshly (1d) emarged fly eye of GMR GAL4

value: control (GMR-GAL4)


title: YQ2 + FBS 1h_rep1

source_name: C. albicans YQ2, RPMI w/ 10% FBS, 1h, replicate 1


title: YL1 - FBS 1h_rep1

source_name: C. albicans YL1, RPMI w/o 10% FBS, 1h, replicate 1


title: YL1 + FBS 1h_rep1

source_name: C. albicans YL1, RPMI w/ 10% FBS, 1h, replicate 1


title: YQ2 - FBS 1h_rep1


title: IL1R1 knockdown_ 24h Mtb infected_ experiment 1_ replicate1

value: Mycobacterium tuberculosis


title: IL1R1 knockdown_ 0h uninfected_ experiment1_ replicate2

source_name: experiment1, IL1R1 knockdown, 0h uninfected


title: IL1R1 knockdown_ 0h uninfected_ experiment1_ replicate1


title: IL36R knockdown_ 0h uninfected_ experiment 1_ replicate2


title: GMR Eye Tm-5 TR1

description: microRNA expression in fly eye

source_name: Freshly (1d) emarged fly eye of GMR GAL4 Fly


title: SF_0007_blood_transcriptome

status: Public on Feb 13 2018

city: Jouy-en-Josas

first: Jordi

last: Estelle

address: Domaine de Vilvert, Bat. GABI-320

country: France

institute: INRAE

description: Gene expression at 60 days of age

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Sus scrofa

source_name: Peripheral Blood

growth_protocol: Pigs were reared under standard conditions and were fed a conventional diet ad libitum. All animals were vaccinated against Mycoplasma hyopneumoniae (Stellamune, Pfizer, one injection) at 36 days of age.

extract_protocol: Total blood RNA was isolated using PAXgene Blood RNA Kit (Qiagen, Germany) following manufacturer’s intructions. The RNA purity and concentration were determined using a NanoDrop 1000 spectrophotometer (Thermo Scientific, USA), and the RNA integrity was assessed using the Bioanalyzer 2100 (Agilent Technologies, USA).

treatment_protocol: Blood samples were collected in PaxGen tubes in 60 days-old pigs

value: whole blood

value: 60 days


title: SF_0073_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0308_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0043_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0006_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0586_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0079_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0032_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0327_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0136_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0035_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0049_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0191_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0201_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0232_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0077_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0143_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0080_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0182_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0071_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0157_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0579_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0553_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0552_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0202_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0250_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0207_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0592_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0584_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0217_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0147_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0199_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0547_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0018_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0149_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0218_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0152_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0300_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0058_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0205_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0059_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0449_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0222_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0275_blood_transcriptome

description: Gene expression at 60 days of age


title: IL36R knockdown_ TB24h Mtb infected_ experiment2_ replicate2

source_name: experiment2, IL36R knockdown, TB24h Mtb infected


title: SF_0276_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0277_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0243_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0211_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0440_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0013_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0215_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0322_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0132_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0241_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0082_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0040_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0299_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0278_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0095_blood_transcriptome

description: Gene expression at 60 days of age


title: Sample 4: Muscle, control diet

source_name: Muscle

value: Muscle


title: SF_0212_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0225_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0554_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0017_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0559_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0471_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0546_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0041_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0251_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0140_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0340_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0144_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0236_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0530_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0328_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0069_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0262_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0318_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0525_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0288_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0574_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0204_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0558_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0011_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0531_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0519_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0294_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0033_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0009_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0031_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0532_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0517_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0226_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0155_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0319_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0317_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0295_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0248_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0255_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0405_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0315_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0302_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0025_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0480_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0034_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0265_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0261_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0545_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0247_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0524_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0526_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0245_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0067_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0051_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0027_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0266_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0544_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0151_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0591_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0137_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0448_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0072_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0090_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0070_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0038_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0145_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0096_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0008_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0273_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0193_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0052_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0037_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0583_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0023_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0046_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0569_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0214_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0183_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0081_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0054_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0589_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0549_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0146_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0198_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0292_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0578_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0339_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0016_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0342_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0138_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0496_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0523_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0030_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0561_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0259_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0470_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0254_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0053_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0595_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0439_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0338_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0280_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0274_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0568_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0233_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0306_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0142_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0538_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0529_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0312_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0050_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0264_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0527_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0573_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0083_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0258_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0528_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0048_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0244_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0187_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0055_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0590_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0057_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0452_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0560_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0156_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0012_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0133_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0064_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0535_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0493_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0186_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0332_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0062_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0596_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0267_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0269_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0282_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0209_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0180_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0271_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0104_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0520_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0141_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0513_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0321_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0101_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0303_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0028_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0210_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0458_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0305_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0548_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0131_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0311_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0024_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0063_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0103_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0019_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0150_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0485_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0042_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0092_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0242_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0074_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0230_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0320_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0310_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0353_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0093_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0229_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0539_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0039_blood_transcriptome

description: Gene expression at 60 days of age


title: UA159_XIP3

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

description:
enriched mRNA
repeat 3 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Genome_build: NC_004350.2
Supplementary_files_format_and_content: Counts obtained from step 6: htseq-count, listed along side each open reading frame

organism: Streptococcus mutans

source_name: Whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in FMC medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

tag: background strain

value: 2 uM sXIP at OD600 nm= 0.2, OD600 nm = 0.5

tag: genotype

value: wildtype


title: XrpA_DMSO2

description:
enriched mRNA
repeat 2 of 3


title: XrpA_DMSO3

description:
enriched mRNA
repeat 3 of 3


title: UA159_XIP1

description:
enriched mRNA
repeat 1 of 3


title: XrpA_DMSO1

description:
enriched mRNA
repeat 1 of 3


title: UA159_XIP2

description:
enriched mRNA
repeat 2 of 3


title: SF_0585_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0272_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0518_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0148_blood_transcriptome

description: Gene expression at 60 days of age


title: UA159_DMSO2

description:
enriched mRNA
repeat 2 of 3


title: SF_0056_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0454_blood_transcriptome

description: Gene expression at 60 days of age


title: UA159_DMSO1

description:
enriched mRNA
repeat 1 of 3


title: SF_0154_blood_transcriptome

description: Gene expression at 60 days of age


title: UA159_DMSO3

description:
enriched mRNA
repeat 3 of 3


title: SF_0555_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0004_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0047_blood_transcriptome

description: Gene expression at 60 days of age


title: SF_0514_blood_transcriptome

description: Gene expression at 60 days of age


title: Uninfected rep3

city: Gaithersburg

first: Taylor

last: Cohen

state: MD

address: One Medimmune Way

institute: MedImmune

hyb_protocol: The biotin-labeled aRNA was purified with RNA binding beads and then fragmented at 94°C for 35 min in fragmentation buffer (40 mM Tris-acetate, pH 8.2, 100 mM Potassium Acetate and 30 mM Magnesium Acetate). Fragmented aRNA (10 µg) was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) at 45 °C for 18 hrs.

scan_protocol: Affymetrix GeneChip Fluidics Station 450 was used for washing and staining of the arrays, and hybridized arrays were scanned using a GeneChip Scanner 300 7G (Thermo Fisher Scientific) according to the manufacturer’s user guide.

data_processing: Array files were normalized using the RMA method, and analyzed with Limma for differential expression analysis and GAGE for gene set (pathway) enrichment.

source_name: Alveolar macrophages uninfected control

label_protocol: Briefly, 75 ng of total RNA was reverse transcribed to first strand cDNA with T7-oligo(dT) primer using ArrayScript reverse transcriptase, followed by second strand cDNA synthesis to generate double-stranded cDNA (ds-cDNA). Subsequently, the ds-DNA was used as a template for in vitro transcription to synthesize biotin-labeled antisense-RNA (aRNA) molecules.

extract_protocol: Alveolar macrophages were purified from the BAL of naïve and infected mice by CD11c bead selection (Stem Cell). Cells purified from 10 mice were pooled and treated as a single sample for analysis. Total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol and treated with RNase-free DNase I to remove genomic DNA contamination. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and the quality of RNA was assessed using the Agilent RNA ScreenTape assay in conjunction with a 4200 TapeStation system (Agilent Technologies). Only high-quality RNA samples with an RNA Integrity Number (RIN) greater than 9 were used for microarray hybridization.

treatment_protocol: Specific-pathogen-free 7- to 8-week-old female C57BL/6J mice (The Jackson Laboratory, Bar Harbor, ME) were briefly anesthetized and maintained in 3% isoflurane (Butler Schein™ Animal Health) with oxygen at 3 L/min and infected intranasally (S. aureus USA300 strain SF8300). All bacterial suspensions were administered in 50 µL of PBS. MEDI4893* (LC10) or c-IgG was administered in 0.5 mL intraperitoneally (IP) 24h prior to infection.

tag: strain/background

value: Female

value: 7 weeks

tag: infection

value: Alveolar macrophage


title: Uninfected rep2

tag: gender


title: Anti-AT rep1

source_name: Alveolar macrophages 24h post S. aureus infection, with AT neutralization

value: Anti-alpha toxin

value: Staphylococcus aureus


title: WT [206_1623A]

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized fMouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

source_name: Mouse brain

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Rneasy kit extraction

value: brain

value: WT


title: Control IgG rep1

source_name: Alveolar macrophages 24h post S. aureus infection, without AT neutralization

value: Control IgG


title: Uninfected rep1


title: youngm-3

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

description:
ym-3.txt
mRNA expression in male young bladder

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505B with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid:028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The signal intensity of each probe was normalized by a percentile shift in which each value was divided by the 75th percentile of all values in its array.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The bladder body was dissected out and immediately placed in RNAlater RNA Stabilization Reagent (QIAGEN, Venlo, the Netherland). Total RNA was extracted from tissues using miRNeasy Mini Kit (QIAGEN).

tag: strain

value: male

value: 12 months-old

value: bladder


title: Anti-AT rep2


title: FOXO TKO [433_1623G]

value: FOXO 1/3/4 KO


title: FOXO TKO [212_1623B]


title: FOXO TKO [384_1623C]


title: Control IgG rep3


title: Anti-AT rep3


title: FOXO TKO [386_1623E]


title: WT [MS17_1623M]


title: WT [437_1623I]


title: WT [385_1623D]


title: WT [41_1623F]


title: youngm-2

description:
ym-2.txt
mRNA expression in male young bladder


title: Control IgG rep2


title: FOXO TKO [903_1623K]


title: FOXO TKO [433CA13_1623H]


title: FOXO TKO [390_1586A]


title: FOXO TKO [391_1586B]


title: WT [392_1586C]


title: WT [437CA13_1623J]


title: youngm-4

description:
ym-4.txt
mRNA expression in male young bladder


title: FOXO TKO [MS15_1623L]


title: WT [393_1586D]


title: oldf-4

description:
oldf-4.txt
mRNA expression in old female bladder

value: female

value: 27-30 months-old


title: oldf-3

description:
oldf-3.txt
mRNA expression in old female bladder


title: youngm-1

description:
ym-1.txt
mRNA expression in male young bladder


title: youngf-1

description:
yf-1.txt
mRNA expression in young female bladder


title: youngf-4

description:
yf-4.txt
mRNA expression in young female bladder


title: youngf-2

description:
yf-2.txt
mRNA expression in young female bladder


title: oldm-4

description:
oldm-4.txt
mRNA expression in male old bladder


title: oldm-3

description:
oldm-3.txt
mRNA expression in male old bladder


title: oldf-1

description:
oldf-1.txt
mRNA expression in old female bladder


title: oldf-2

description:
oldf-2.txt
mRNA expression in old female bladder


title: oldm-2

description:
oldm-2.txt
mRNA expression in male old bladder


title: oldm-1

description:
oldm-1.txt
mRNA expression in male old bladder


title: youngf-3

description:
yf-3.txt
mRNA expression in young female bladder


title: Recurence104

city: WARREN

first: nien

last: wei

state: NJ

address: 9 northridge way

institute: Auspex Diagnostics

description: FFPE NSLC

hyb_protocol: The hybridization cocktails contains 3.75 ug of the fragmented, end-labeled cDNA were applied to the Affy Human Gene 2.0 ST arrays. Hybridization was performaed for 17 hours, and the arrays were washed and stained with GeneChip Fluidicd Station 450.

scan_protocol: Arrays were scanned using Affymetrix  GCS 3000 7G and GeneChip Operating sofware v. 1.4 to produce Cel intensity files.

data_processing: Affymetrix Expression Console is used to extract data

source_name: surgical tumor tissue

label_protocol: Samples were fragmented and labeled using NuGen Encore Biotin kit

extract_protocol: Total RNA from patient samples were extracted on the Qiasymphony using Qiasymphony RNA kit

tag: group

value: Had Recurrence


title: Recurence101

description: FFPE NSLC


title: Recurence108

description: FFPE NSLC


title: Recurence110

description: FFPE NSLC


title: Recurence107

description: FFPE NSLC


title: Recurence105

description: FFPE NSLC


title: Recurence99

description: FFPE NSLC


title: Recurence98

description: FFPE NSLC


title: Recurence100

description: FFPE NSLC


title: Recurence95

description: FFPE NSLC


title: Recurence106

description: FFPE NSLC


title: Recurence97

description: FFPE NSLC


title: Recurence109

description: FFPE NSLC


title: Recurence103

description: FFPE NSLC


title: Recurence102

description: FFPE NSLC


title: Recurence94

description: FFPE NSLC


title: Recurence96

description: FFPE NSLC


title: Recurence93

description: FFPE NSLC


title: Recurence84

description: FFPE NSLC


title: Recurence92

description: FFPE NSLC


title: Recurence91

description: FFPE NSLC


title: Recurence90

description: FFPE NSLC


title: Recurence85

description: FFPE NSLC


title: Recurence82

description: FFPE NSLC


title: Recurence88

description: FFPE NSLC


title: Recurence76

description: FFPE NSLC


title: Recurence89

description: FFPE NSLC


title: Recurence83

description: FFPE NSLC


title: Recurence87

description: FFPE NSLC


title: Recurence81

description: FFPE NSLC


title: Recurence79

description: FFPE NSLC


title: Recurence77

description: FFPE NSLC


title: Recurence75

description: FFPE NSLC


title: Recurence80

description: FFPE NSLC


title: Recurence78

description: FFPE NSLC


title: Recurence70

description: FFPE NSLC


title: Recurence69

description: FFPE NSLC


title: Recurence86

description: FFPE NSLC


title: Recurence74

description: FFPE NSLC


title: Recurence72

description: FFPE NSLC


title: Recurence68

description: FFPE NSLC


title: Recurence71

description: FFPE NSLC


title: Recurence73

description: FFPE NSLC


title: Recurence66

description: FFPE NSLC


title: Recurence67

description: FFPE NSLC


title: Recurence65

description: FFPE NSLC


title: Recurence63

description: FFPE NSLC


title: Recurence64

description: FFPE NSLC


title: Recurence61

description: FFPE NSLC


title: Recurence58

description: FFPE NSLC


title: Recurence59

description: FFPE NSLC


title: Recurence60

description: FFPE NSLC


title: Recurence56

description: FFPE NSLC


title: Recurence44

description: FFPE NSLC


title: Recurence51

description: FFPE NSLC


title: Recurence54

description: FFPE NSLC


title: Recurence53

description: FFPE NSLC


title: Recurence41

description: FFPE NSLC


title: Recurence50

description: FFPE NSLC


title: Recurence52

description: FFPE NSLC


title: Recurence55

description: FFPE NSLC


title: Recurence45

description: FFPE NSLC


title: Recurence47

description: FFPE NSLC


title: Recurence49

description: FFPE NSLC


title: Recurence62

description: FFPE NSLC


title: Recurence57

description: FFPE NSLC


title: Recurence48

description: FFPE NSLC


title: Recurence42

description: FFPE NSLC


title: Recurence39

description: FFPE NSLC


title: Recurence43

description: FFPE NSLC


title: Recurence38

description: FFPE NSLC


title: Recurence40

description: FFPE NSLC


title: Recurence46

description: FFPE NSLC


title: Recurence37

description: FFPE NSLC


title: Recurence34

description: FFPE NSLC


title: Recurence35

description: FFPE NSLC


title: Recurence36

description: FFPE NSLC


title: Recurence31

description: FFPE NSLC


title: Recurence32

description: FFPE NSLC


title: Recurence33

description: FFPE NSLC


title: Recurence29

description: FFPE NSLC


title: Recurence28

description: FFPE NSLC


title: Recurence30

description: FFPE NSLC


title: Recurence25

description: FFPE NSLC


title: Recurence26

description: FFPE NSLC


title: Recurence19

description: FFPE NSLC


title: Recurence22

description: FFPE NSLC


title: Recurence27

description: FFPE NSLC


title: Recurence21

description: FFPE NSLC


title: Recurence20

description: FFPE NSLC


title: Recurence16

description: FFPE NSLC


title: Recurence23

description: FFPE NSLC


title: Recurence13

description: FFPE NSLC


title: Recurence18

description: FFPE NSLC


title: Recurence24

description: FFPE NSLC


title: Recurence15

description: FFPE NSLC


title: Recurence17

description: FFPE NSLC


title: Recurence12

description: FFPE NSLC


title: Recurence14

description: FFPE NSLC


title: Recurence11

description: FFPE NSLC


title: Recurence9

description: FFPE NSLC


title: Recurence10

description: FFPE NSLC


title: Recurence7

description: FFPE NSLC


title: Recurence4

description: FFPE NSLC


title: Recurence6

description: FFPE NSLC


title: Recurence8

description: FFPE NSLC


title: Recurence5

description: FFPE NSLC


title: Recurence1

description: FFPE NSLC


title: NonRecurence101

description: FFPE NSLC

value: No Recurrence during follow-up


title: NonRecurence100

description: FFPE NSLC


title: NonRecurence97

description: FFPE NSLC


title: NonRecurence99

description: FFPE NSLC


title: NonRecurence96

description: FFPE NSLC


title: NonRecurence98

description: FFPE NSLC


title: NonRecurence95

description: FFPE NSLC


title: Recurence3

description: FFPE NSLC


title: NonRecurence91

description: FFPE NSLC


title: NonRecurence93

description: FFPE NSLC


title: NonRecurence92

description: FFPE NSLC


title: NonRecurence94

description: FFPE NSLC


title: NonRecurence90

description: FFPE NSLC


title: NonRecurence79

description: FFPE NSLC


title: NonRecurence86

description: FFPE NSLC


title: NonRecurence87

description: FFPE NSLC


title: NonRecurence89

description: FFPE NSLC