title: Infected_48h pi_Rep2

description:
SAMPLE 6B
miRNA microarray data.

tag: treatment


title: Infected_48h pi_Rep1

status: Public on Jan 01 2015

type: RNA

city: FARIDABAD

first: ARUP

last: BANERJEE

state: Haryana

address: THSTI, 3RD MILE STONE, FARIDABAD GURGAON EXPRESSWAY, NCR BIOTECH CLUSTER

department: VIDRC

country: India

institute: TRANSLATIONAL HEALTH SCIENCE & TECHNOLOGY INSTITUTE

description:
SAMPLE 6A
miRNA microarray data.

hyb_protocol: Complex probes were hybridized to each GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix).

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

data_processing: Scanned images of microarray chips were analyzed using Affymetrix Expression Console with the default RMA settings. Raw data were processed and normalized on basis of organism human using RMA algorithm. The normalized data (CHP files) processed for the differential miRNA analysis in Affymetrix TAC software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CHME3 cells grown on transwells, infected with JEV, 48h pi

label_protocol: Complex probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: CHME3 cells grown on 6-well plates.

extract_protocol: Total RNA prepared using Qiagen RNA extraction kit.

treatment_protocol: Infected with an MOI of 5 pfu/cell of Japanese encephalitis virus (P20778 strain).

tag: cell line

tag: cell type

value: microglial cell line

tag: cell state

value: polarized

value: Japanese encephalitis virus strain P20778 infection

tag: time point

value: 48h post infection


title: Uninfected_48h pi_Rep2

description:
SAMPLE 5B
miRNA microarray data.

source_name: CHME3 cells grown on transwells, mock infected, 48h pi

value: mock infected


title: SLE patient, 1034V2

city: Indianapolis

first: Robert

middle: W

last: Hoffman

state: IN

address: Lilly Corporate Center

department: Lilly Bio-Medicines/Immunology

country: USA

institute: Eli Lilly and Company

description: Gene expression data from RNP autoantibody+ SLE patient blood

hyb_protocol: The cDNA generated during the amplification step was used in a fragmentation and labeling reaction to generate target for hybridization to the Affymetrix Human GeneChip® HU133 Plus 2.0.

data_processing: The data were analyzed with Partek Genomics Suite using the Affymetrix default analysis settings. RMA background correction and quantile normalization were applied with the median polish approach for summarizing probe sets.

source_name: SLE patient blood

label_protocol: Not provided

extract_protocol:
Extraction of total RNA was performed using the Qiagen RNeasy Plus kit according to the manufacturer's instructions.
A custom, automated version of the NuGEN Ovation v2.0 WB amplification system was used for RNA extracted from blood.

tag: diagnosis

value: systemic lupus erythematosus (SLE)

tag: tissue

value: blood


title: Infected_24h pi_Rep2

description:
SAMPLE 4B
miRNA microarray data.

source_name: CHME3 cells grown on transwells, infected with JEV, 24h pi

value: 24h post infection


title: Uninfected_48h pi_Rep3

description:
SAMPLE 5C
miRNA microarray data.


title: Infected_24h pi_Rep3

description:
SAMPLE 4C
miRNA microarray data.


title: Uninfected_48h pi_Rep1

description:
SAMPLE 5A
miRNA microarray data.


title: SLE patient, 1029V2


title: SLE patient, 1030V2


title: SLE patient, 1030V1


title: Uninfected_24h pi_Rep3

description:
SAMPLE 3C
miRNA microarray data.

source_name: CHME3 cells grown on transwells, mock infected, 24h pi


title: SLE patient, 1029V1


title: Infected_24h pi_Rep1

description:
SAMPLE 4A
miRNA microarray data.


title: SLE patient, 1028V1


title: Uninfected_24h pi_Rep2

description:
SAMPLE 3B
miRNA microarray data.


title: SLE patient, 1026V4


title: Infected_6h pi_Rep3

description:
SAMPLE 2C
miRNA microarray data.

source_name: CHME3 cells grown on transwells, infected with JEV, 6h pi

value: 6h post infection


title: Infected_6h pi_Rep2

description:
SAMPLE 2B
miRNA microarray data.


title: SLE patient, 1025V1


title: Uninfected_6h pi_Rep2

description:
SAMPLE 1B
miRNA microarray data.

source_name: CHME3 cells grown on transwells, mock infected, 6h pi


title: SLE patient, 1020V1


title: Infected_6h pi_Rep1

description:
SAMPLE 2A
miRNA microarray data.


title: Uninfected_6h pi_Rep1

description:
SAMPLE 1A
miRNA microarray data.


title: SLE patient, 1024V1


title: SLE patient, 1015V1


title: SLE patient, 1023V1


title: SLE patient, 1021V1


title: Uninfected_6h pi_Rep3

description:
SAMPLE 1C
miRNA microarray data.


title: SLE patient, 1024V2


title: SLE patient, 1012V1


title: SLE patient, 1014V1


title: Ulcerative colitis miRNA in colon mucosa 395

city: Houston

first: R.

middle: Alan

last: Harris

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Ulcerative colitis colon mucosa sample

hyb_protocol: Fluidics Protocol FS450-0003

scan_protocol: Affymetrix Genechip Scanner 7G

data_processing: The Affymetrix Expression Console was used to generate RMA-DABG normalized miRNA expression levels.

source_name: colon mucosa 395

label_protocol: Genisphere FlashTag HSR

extract_protocol: Qiangen/Qiazol - miRNA Isolation Kit

treatment_protocol: Flash freezing of biopsy samples on dry ice

tag: gender

value: Female

tag: age

value: Colon mucosa

tag: disease state

value: Ulcerative colitis


title: SLE patient, 1019V1


title: normal miRNA in colon mucosa 429

description: Normal colon mucosa sample

source_name: colon mucosa 429

value: Male

value: normal


title: normal miRNA in colon mucosa 434

description: Normal colon mucosa sample

source_name: colon mucosa 434


title: Ulcerative colitis miRNA in colon mucosa 432

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 432


title: Ulcerative colitis miRNA in colon mucosa 416

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 416


title: Ulcerative colitis miRNA in colon mucosa 419

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 419


title: Ulcerative colitis miRNA in colon mucosa 397

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 397


title: SLE patient, 1014V2


title: D-HEp3 cells in vivo biological replicate 2

city: New York

first: Julio

middle: Alberto

last: Aguirre-Ghiso

state: NY

address: One Gustave L Levy Place

department: Medicine and Otolaryngology

institute: Ichan School of Medicine at Mount Sinai

hyb_protocol: This step was performed following the hybridization,wash, and stain GeneChip kit from Affymetrix following its manuals.

scan_protocol: For scanning we followed the protocols delineated in the Expression Wash, Stain and Scan User Manual for Cartridge Arrays from Affymetrix

data_processing: Raw CEL file data from Affymetrix GeneChip Operating Software (GCOS) was imported into a Bioconductor session using the Affymetrix package. The batch was background corrected, normalized, and summarized using both gcrma and mas5 functions in parallel. Linear models of differential expression were fit to each of the transformed data sets, and contrasts were estimated between each group of T-HEp3-GFP and D-HEp3-GFP samples. Probability values of the F-statistic were used to gauge the likelihood a gene was significantly differentially expressed. The distributions of the F-statistic P value as determined by the classify TestsF function of the limma package were examined, and a cutoff of significance was established at the inflection point of 0.05 occurring in both transformed sets. Genes significant in gcRMA sets at this level were marked as significant.

source_name: D-HEp3 cells in vivo 7 days xenotransplanted in chick embryos at E10

label_protocol: Labeling protocols followed the standard procedures delineated by the Affymetrix manuals. (2005-2009 Affymetrix Inc.) Biotinylated cRNA was prepared following the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Proliferative T-HEp3-GFP and dormant D-HEp3-GFP cells were inoculated on 10 days old chicken embryo CAMs and after one week growing T-HEp3-GFP tumors or dormant D-HEp3-GFP nodules were surgically removed.

extract_protocol: For RNA extraction from FACS sorted GFP+ cells we followed the following protocol. Briefly, 1ml Trizol/plate, pipett a few times. RT 5min. store at -80C. Thaw, add 200 ul chloroform/ml, shake by hand for 15 sec. Incubate 3 minutes at RT. Centrifuge 14,000 RPM for15 minutes.Transfer upper phase (< 600 ul) to new tube. Add 0.5ml isoproponal and 2ul (10ug) glycogen, mix up and down. Precipitate at -20C for 30min or overnight. Centrifuge 14,000 for 30 minutes. Wash with 1ml 70% ethanol by vortex briefly, centrifuge 12,000 RPM for 10 mins. Wash again. Decant and air dry 5-10mins.  Add 20-60ul RNase free water per well of 6well plate. Fast freeze in liquid N2 then slowly thaw on ice; or freeze in -80C overnight. Nano drop to determine concentration. (260/280=2 (1.8 for DNA), 260/230 from 2.0-2.2). Run Bioanalyzer for full RNA QC. Store RNA sample in -80C.

tag: in vivo phenotype

value: DORMANT


title: SLE patient, 1005V1


title: T-HEp3 cells in vivo biological replicate 2

source_name: T-HEp3 cells in vivo 7 days xenotransplanted in chick embryos at E10

value: PROLIFERATIVE


title: Uninfected_24h pi_Rep1

description:
SAMPLE 3A
miRNA microarray data.


title: T-HEp3 cells in vivo biological replicate 1


title: D-HEp3 cells in vivo biological replicate 3


title: D-HEp3 cells in vivo biological replicate 1


title: normal miRNA in colon mucosa 206

description: Normal colon mucosa sample

source_name: colon mucosa 206


title: SLE patient, 1004V1


title: SOX11-ChIP Z138 2

type: genomic

city: Barcelona

first: Virginia

last: Amador

address: Rossello 153

country: Spain

institute: IDIBAPS

description: Chip-chip Z138 cells SOX11

hyb_protocol: Hybridization to NimbleGen Human ChIP-chip 2.1 M Deluxe Promoter array (Roche NimbleGen) (http://www.nimblegen.com/products/chip/index.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Row data was analyzed for peaks (significant regions of SOX11 enrichment) using NimbleScan v2.4 software and data were visualized in SignalMap v1.9 software.
Genomic fragments with FDR<0.1 and Peak Score>0.5 that overlapped across three independent biological replicates in Z138 SOX11ChIP-chip experiments and were not present in the JVM2 SOX11 ChIP-chip experiment were considered SOX11-ChIP enriched/-bound regions.

molecule: genomic DNA

source_name: SOX11-ChIP DNA from Z138 MCL cell line

label_protocol: Amplified immunoprecipitated (SOX11) and input DNA (9.5µg) from Z138 and JVM2 cell lines were quality controlled, quantified, and sent to NimbleGen System for probe labeling

growth_protocol: cultured in RPMI 1640 medium, supplemented with 10% fetal bovine serum, 2 µM L-glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol: Z138and JVM2 cell lines (5X 107 cells) were fixed with 1% formaldehyde in culture medium for 10 minute at RT followed by quenching with 0.125 M glycine for 5 min. Cells were washed twice with ice-cold PBS and nuclei were isolated by incubation with ChIP buffer (25mM HEPES pH 8.0, 1.5 mM MgCl2, 10 mM KCl, 0.1 % Nonidet-P40, and 1mM DTT) for 10 min at 4°C. Nuclei were resuspended in 1 ml of lysis buffer (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1 % SDS and 0.1% Na-deoxycholate) and sonicated on ice with a Branson Sonifier 250 (20 X 20 seconds, duty 20%, output control 7, hold on ice 1 minute between pulses) followed by sonication using BiorupterTM sonicator from Diagenode (20 cycles of [40 seconds “ON”/ 20 seconds “OFF”]). Sonicated fragments ranged in size from 200-1000 bp. After a spinning step to reduce debris, 10µg of anti-SOX11 antibody (goat C-20; sc-17347; Santa Cruz Biotechnology) was used to immunoprecipitate protein-DNA complexes O/N at 4°C and collected using DNA-saturated Protein G SepharoseTM 4 Fast Flow (GE Healthcare) for 2 hours. After incubation, the immunocomplexes were washed sequentially with low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20mM Tris-HCl, at pH 8.0 and 150mM NaCl), high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, at pH 8.0, and 500mM NaCl), LiCl wash buffer (0.25M LiCl, 1% NP-40, 1% Na-deoxycholate, 1mM EDTA and 10 mM Tris-HCl, at pH 8.0) and TE buffer (10mM Tris-Cl, at pH 8.0, and 1 mM EDTA). Immunocomplexes were eluted in ChIP elution buffer (1% SDS and 0.1 M NaHCO3), the crosslinking was reverted by addition of 5 M NaCl and incubation at 65°C for at least 4 hours and DNA was precipitated with ethanol O/N at -20°C. Samples were then treated with Proteinase K solution (1 M Tris-HCl at pH 6.5, 0.5 M EDTA and proteinase K 10mg/ml) at 45°C for 2 hours and DNA purified using QIAquick® PCR Purification Kit (QIAGEN). 10 ng purified DNA (SOX11-ChIP and Input from Z138 and JVM2 cells) was amplified in two steps using a GenomePlex® Whole Genome Amplification WGA Kit (Sigma), following the manufacturer’s instructions and used for ChIP-chip analysis and/or ChIP-qPCR.  We performed ChIP assays in triplicate from Z138 cell line expressing SOX11 and in a single experiment from JVM2 cell line as negative control.

tag: chip antibody

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #

source_name: imput DNA from Z138.2

value: none, input DNA


title: SLE patient, 1011V1

source_name: SLE patient blood


title: ftsZ Depletion Cells Uninduced 2hr Replicate 2

first: Jue

middle: D.

last: Wang

address: 1 Baylor Plaza, Rm T932

description: Biological replicate 2 of 4. FtsZ uninduced 2hr

hyb_protocol: The procedure for hybridization was performed as described previously (Britton et al., 2002).

scan_protocol: Scanned on a GenePix 4000B Scanner (Axon Instruments).

data_processing: GenePix Pro (v 6.1) was used for background subtraction and normalization.

organism: Bacillus subtilis

source_name: ftsZ depletion

label_protocol: The procedures for reverse transcription and labeling were performed as described previously (Britton et al., 2002).

growth_protocol: Pxyl-ftsZ cells were grown to mid-exponential phase (OD600 0.2-0.6) in LB with 0.5% xylose at 37°C with shaking.

extract_protocol: RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions.

treatment_protocol: Pxyl-ftsZ cells were washed twice in LB and then grown without the addition of 0.5% xylose for 1 or 2hrs (to block division) or with 0.5% xylose (to allow normal cell division)

value: Not induced for 2hr

source_name: pooled reference RNA

tag: sample type

value: Pooled RNA from mixture of the same amount of wt standards


title: ftsZ Depletion Cells Uninduced 2hr Replicate 4

description: Biological replicate 4 of 4. FtsZ uninduced 2hr


title: ftsZ Depletion Cells Uninduced 2hr Replicate 3

description: Biological replicate 3 of 4. FtsZ uninduced 2hr


title: ftsZ Depletion Cells Uninduced 2hr Replicate 1

description: Biological replicate 1 of 4. FtsZ uninduced 2hr


title: ftsZ Depletion Cells Induced 2hr Replicate 4

description: Biological replicate 4 of 4. FtsZ induced 2hr

value: Induced for 2hr


title: ftsZ Depletion Cells Induced 2hr Replicate 3

description: Biological replicate 3 of 4. FtsZ induced 2hr


title: ftsZ Depletion Cells Uninduced 1hr Replicate 3

description: Biological replicate 3 of 3. FtsZ uninduced 1hr

value: Not induced for 1hr


title: SLE patient, 1001V1

value: systemic lupus erythematosus (SLE)


title: FEPS without daunirubicin replicate 2

city: Rio de Janeiro

first: Miguel

middle: Angelo Martins

last: Moreira

state: Riio de Janeiro

address: André Cavalcanti, 37

department: Genetics Program

country: Brazil

institute: Instituto Nacional de Câncer

description:
Gene expression data
FEPS.2-DAUNO

scan_protocol: Chips were scaned with Affymetrix Gene Chip Scanner 3000, according to the standard Affymetrix protocol

data_processing: Affymetrix Expression Console, using 3' expression arrays-rma analysis

label: Biotin

source_name: FEPS1 grown in RMPI 1640 medium with 10% FBS and 5% CO2 at 37oC, maintained in medium without drugs for seven days

growth_protocol: cell lines were grown in RPMI 1640 with 10% SFB and 5% CO2, and with the respective drug (vincristine or daunorubicin) when required.

extract_protocol: Total RNA were isolated with Rneasy mini Kit (Qiagen) from 5 X10E6 to 1 X10E7 cells

treatment_protocol: cell with multdrug resistence phenotype were growed for seven days in culture medium without drugs (vincristine or daunorubicin) for seven days

value: FEPS

tag: cell line origin

value: Cell line derived from K562, selected for resistance to daunorubicin and with multidrug resentance phenotype, grown without daunorubicin

tag: agent

value: without daunorubicin


title: SOX11-ChIP Z138 3

description: Chip-chip Z138 cells SOX11

source_name: imput DNA from Z138.3


title: SLE patient, 1001V2

value: blood


title: FEPS without daunirubicin replicate 1

description:
Gene expression data
FEPS.1-DAUNO

hyb_protocol: according to the standard Affymetrix protocol


title: SOX11-ChIP Z138 1

description: Chip-chip Z138 cells SOX11

source_name: imput DNA from Z138.1


title: FEPS with daunorubicin replicate 2

description:
Gene expression data
FEPS.2+DAUNO

source_name: FEPS1 grown in RMPI 1640 medium with 10% FBS and 5% CO2 at 37oC, with 466nM daunorrubicin

label_protocol: according to the standard Affymetrix protocol

value: Cell line derived from K562, selected for resistance to daunorubicin and with multidrug resentance phenotype, grown in the presence of daunorubicin

value: daunorubicin


title: ftsZ Depletion Cells Induced 2hr Replicate 2

description: Biological replicate 2 of 4. FtsZ induced 2hr

tag: treatment


title: ftsZ Depletion Cells Induced 2hr Replicate 1

description: Biological replicate 1 of 4. FtsZ induced 2hr


title: ftsZ Depletion Cells Uninduced 1hr Replicate 2

description: Biological replicate 2 of 3. FtsZ uninduced 1hr


title: SOX11-ChIP JVM2

description: Chip-chip JVM2 cells SOX11

source_name: SOX11-ChIP DNA from JVM2 MCL cell line

tag: cell line

source_name: imput DNA from JVM2


title: T-HEp3 cells in vivo biological replicate 3

tag: cell type


title: ftsZ Depletion Cells Uninduced 1hr Replicate 1

description: Biological replicate 1 of 3. FtsZ uninduced 1hr


title: Spermatozoa_NS3_rep1

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

description:
NS3
Gene expression alterations in human control spermatozoa

hyb_protocol: Cy3-labelled cRNA was hybridize using the manufacter's protocole (miRNA Microarray System with miRNA Complete labelling and Hyb kit).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, 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 miRNA_107_Sept09_patch and Grid: US83700202_253118111117_S01_grid) to obtain background subtracted and spatially detrended Processed Signal intensities. To reduce the effect of noise in the miRNA microarrays data, we aggregated probes signals to have a more robust measure of expression, by computing the median of the intensity values (gProcessedSignal) of the set of probes corresponding to each miRNA. The samples were then normalized by the quantile method.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared according to the miRNA Microarray System with miRNA Complete labelling.

extract_protocol: Subsequent to storage, samples were thawed and washed twice in 2 ml of PBS, then suspended in round cell lysis buffer (0.1% SDS, 0.5% Triton X-100 in RNase free H2O). RNA was extracted using the RNeasy mini kit (Qiagen GmbH., Germany) with gentle modifications. Sperm cells were suspended in 600 µl of lysis buffer for 107 cells. This cell suspention was lysed using a Politron as previously described (Saade, et al., 2007), to maximize the recovery of spermatozoal RNA. The lysates were then processed according to the manufacturer’s instructions using the animal cell protocol. After RNase-free DNase treatment (Qiagen GmbH., Germany), the RNA was eluted with 30µl.  RNA concentration was determined using a nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: male

tag: age (years)

tag: status

value: non-smoker

tag: spermatozoa (m/ml)

tag: round cells (m/ml)

tag: motility (a/b/c/d)

tag: % normal forms

tag: cigarette/day (starting year)


title: Spermatozoa_NS2_rep1

description:
NS2
Gene expression alterations in human control spermatozoa

tag: gender


title: Spermatozoa_NS1_rep1

description:
NS1
Gene expression alterations in human control spermatozoa


title: ftsZ Depletion Cells Induced 1hr Replicate 2

description: Biological replicate 2 of 3. FtsZ induced 1hr

value: Induced for 1hr


title: ftsZ Depletion Cells Induced 1hr Replicate 1

description: Biological replicate 1 of 3. FtsZ induced 1hr


title: Spermatozoa_S4_rep1

description:
S4
Tobacco-induced gene expression alterations in human spermatozoa

value: smoker


title: Spermatozoa_NS4_rep1

description:
NS4
Gene expression alterations in human control spermatozoa


title: Spermatozoa_S2_rep1

description:
S2
Tobacco-induced gene expression alterations in human spermatozoa


title: Lucena 1 without vincristine replicate 2

description:
Gene expression data
LUCENA1.2 -VCR

source_name: LUCENA1 grown in RMPI 1640 medium with 10% FBS and 5% CO2 at 37oC, maintained in medium without drugs for seven days

value: Lucena 1

value: Cell line derived from K562, selected for resistance to vincristine and with multidrug resentance phenotype, grown without vincristine

value: without vincristina


title: Spermatozoa_S1_rep1

description:
S1
Tobacco-induced gene expression alterations in human spermatozoa


title: Lucena 1 without vincristine replicate 1

description:
Gene expression data
LUCENA1.1 -VCR


title: Lucena 1 with vincristina replicate 2

description:
Gene expression data
LUCENA1.2+VCR

source_name: LUCENA1 grown in RMPI 1640 medium with 10% FBS and 5% CO2 at 37oC, with 60nM vincristine

value: Cell line derived from K562, selected for resistance to vincristine and with multidrug resentance phenotype, grown in the presence of vincristine

value: vincristina


title: K562 replicate 2

description:
Gene expression data
K562.2

source_name: K562 grown in RMPI 1640 medium with 10% FBS and 5% CO2 at 37oC

value: Cell line derived from a patient with chronic myeloid leukemia; drug-sensitive cell line.

value: control


title: Spermatozoa_S3_rep1

description:
S3
Tobacco-induced gene expression alterations in human spermatozoa


title: Lucena 1 with vincristina replicate 1

description:
Gene expression data
LUCENA1.1+VCR


title: human_lungEC-control_VEGF_24h

city: Tokyo

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

country: Japan

institute: The University of Tokyo

description: human lungEC-control VEGF 24h

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45 degree Celsius, 16 hours). Hybridization was controlled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: GeneChip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: lung endothelial cells, Ad-cont VEGF, 24h

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

value: primary cultured lung endothelial cells

tag: transfection

value: control adenovirus

value: VEGF

tag: treatment duration


title: human_lungEC-Ad-DSCR1_VEGF1h

description: human lungEC-Ad-DSCR1_VEGF1h

source_name: lung endothelial cells, Ad-DSCR1 VEGF, 1h

value: DSCR-1 adenovirus


title: human_lungEC-Ad-DSCR1_VEGF0h

description: human lungEC-Ad-DSCR1_VEGF0h

source_name: lung endothelial cells, Ad-DSCR1 VEGF, 0h


title: human_lungEC-Ad-DSCR1_VEGF4h

description: human lungEC-Ad-DSCR1_VEGF4h

source_name: lung endothelial cells, Ad-DSCR1 VEGF, 4h


title: human_lungEC-Ad-DSCR1_VEGF24h

description: human lungEC-Ad-DSCR1_VEGF24h

source_name: lung endothelial cells, Ad-DSCR1 VEGF, 24h


title: K562 replicate 1

description:
Gene expression data
K562.1


title: human_lungEC-control_VEGF1h

description: human lungEC-control VEGF1h

source_name: lung endothelial cells, Ad-cont VEGF, 1h


title: human_lungEC-control_VEGF_4h

description: human lungEC-control VEGF 4h

source_name: lung endothelial cells, Ad-cont VEGF, 4h


title: human_lungEC-control_VEGF0h

description: human lungEC-control VEGF0h

source_name: lung endothelial cells, Ad-cont VEGF, 0h


title: 006-L1 ApoE-/- Timp3-/-

type: SRA

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

library_source: transcriptomic

data_processing:
We applied a pipeline combining TopHat (http://tophat.cbcb.umd.edu) and Cufflinks(http://cuffinks.cbcb.umd.edu) to identify transcripts in each sample. Tophat (Trapnell et al, 2009) uses Bowtie aligner (Langmead et al, 2009) to produce align ment and to discover splice junctions. Cuffinks (Trapnell et al, 2010) assembles transcripts, estimates their abundances, and tests for differential expression and regulation. Reads were aligned against the mouse reference genome (NCBIM37.60) and the identified transcripts were compared to those annotated in the reference genome.
The metric used by Cuffinks to estimate the abundance of transcripts is the FPKM: Fragments Per Kilobase of exon per Million fragments mapped. The FPKM was introduced by (Trapnell et al, 2010)
Genome_build: NCBIm37
Supplementary_files_format_and_content: GTF files containing isoforms assembled by Cufflinks before Cuffmerge processing. There is one record per row, and each record represents either a transcript or an exon within a transcript

organism: Mus musculus

source_name: heart

extract_protocol:
Total RNA was isolated from mice hearts of ApoE-/- and ApoE-/-Timp3-/- using Trizol reagent (Invitrogen Corp, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: heart

tag: age

value: 32 weeks

tag: genotype/variation

value: ApoE-/- Timp3-/-


title: 005-L1 ApoE-/- Timp3-/-


title: human_lungEC-DSCR-1_KD_2

description: human lungEC-DSCR-1KD

source_name: lung endothelial cells, si-DSCR-1

value: DSCR-1 siRNA


title: CRTC1 n4

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description:
Sample name: 8_CRTC1
Gene expression data from Caco-2 epithelial colonic tumor cell with CRTC1 overexpression.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 2.0 ST Arrays. Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

source_name: Caco-2, CRTC1 overexpression

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip Whole Transcript (WT) Sense Target labelling assay kit Affymetrix).

growth_protocol: Caco-2 clone TC7 cells (kind gift of Monique Rousset, Paris, France) were grown in DMEM High Glucose (4.5g/l) medium supplemented with 10% serum and 1% penicillin/streptomycin.

extract_protocol: Isolation of mRNA from cultured cells were performed by using RNeasy Mini Kit (Qiagen).

treatment_protocol: Subconfluent Caco-2 cells were transfected with 200ng of CRTC1 expression plasmid or corresponding empty vector (pBS) overnight.

value: epithelial colonic tumor cell line

tag: expression vector


title: 004-L1 ApoE-/- Timp3-/-


title: 003-L1 ApoE-/-

value: ApoE-/-


title: CRTC1 n3

description:
Sample name: 6_CRTC1
Gene expression data from Caco-2 epithelial colonic tumor cell with CRTC1 overexpression.


title: 002-L1 ApoE-/-


title: CTRL n4

description:
Sample name: 7_pBS
Gene expression data from Caco-2 epithelial colonic tumor cell control sample.

source_name: Caco-2, control

value: empty


title: 001-L1 ApoE-/-


title: CTRL n2

description:
Sample name: 3_pBS
Gene expression data from Caco-2 epithelial colonic tumor cell control sample.


title: human_lungEC-control_1

description: human lungEC-control

source_name: lung endothelial cells, si-cont

value: control siRNA


title: human_lungEC-DSCR-1_KD_1

description: human lungEC-DSCR-1 KD


title: Wild Type, no leptin, biological replicate 3

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

hyb_protocol: Three biological replicates of each sample were hybridized to Human Genome U133 Plus 2.0 gene chips (Affymetrix).

scan_protocol: Scanned using the GeneChip Scanner 3000 7G (AffyMetrix).

data_processing: Data extraction, QC, and GCRMA normalization were performed with BioConductor software.  Differential expression was assessed with moderated ANOVA, using the BioConductor limma package; false discovery rate (FDR) estimates were calculated using the Benjamini-Hochberg method.

source_name: Wild Type, no leptin

label_protocol: Total RNA was amplified and converted to cDNA using the 3' IVT Express Kit (Affymetrix).

growth_protocol: HEK293T/17 cells were maintained in a humidified incubator at 37 °C with 5% CO2. HEK293T/17 cells were cultured in DMEM/F12 (Gibco) with non-essential amino acids, sodium pyruvate and 10% heat inactivated FBS.  Jurkat T-cells were cultured in RPMI supplemented with 10% heat inactivated FBS.  Caco-2 cells were cultured in EMEM (Gibco) supplemented with non-essential amino acids, sodium pyruvate and 20% heat inactivated FBS.  Cells were discarded after passage 25 and new cultures were started from frozen stocks. HEK293T117 cells were transiently transfected using lipofectamine 2000 per the product instructions (Invitrogen, Carlsbad, CA). The plasmids mLEPRb/pCDNA3 (47), mLEPRbR223/pCDNA3 (35) and LEPRbDelta65/pCDNA3 (47) were obtained from Martin Myers and have been described previously as referenced. pCDNA3 was used as a vector control. The plasmid mLEPRb/pCDNA3 was used as a template for site-directed mutagenesis to construct mLEPRb985L/pCDNA3, LEPRb1077L/pCDNA3 and mLEPRb1138L/pCDNA3.  Site-directed mutagenesis was done using the quikchange kit (Stragene/Agilent, Santa Clara, CA).    The presence of the desired mutations and the absence of other mutations were confirmed by DNA sequencing.

extract_protocol: RNA was prepared using RNeasy Mini kit (QIAGEN) and its quality was verified in an Agilent Bioanalyzer.

treatment_protocol: HEK293 cells were transfected with WT LepR or Y1138L (STAT3-mutant) leptin receptor.  48 hours post-transfection cells were made quiescent by incubation in optimum plus 0.5% BSA for 3 hours.  Cells were then stimulated with 100ng of leptin or maintained in optimum plus 0.5% BSA for an additional 3 hours. Leptin was purchased from Dr. A.F. Parlow, National Hormone and Peptide Program (Torrance, CA). The STAT3 inhibitor, Stattic, the PI3K inhibitor, LY294002 and the MEK inhibitor PD98059 were purchased from EMD chemicals (Gibbstown, NJ).

value: Wild-type leptin receptor

tag: treatment

value: untreated


title: CRTC1 n2

description:
Sample name: 4_CRTC1
Gene expression data from Caco-2 epithelial colonic tumor cell with CRTC1 overexpression.

tag: cell line


title: human_lungEC-control_2

description: human lungEC-control

tag: cell type


title: CTRL n1

description:
Sample name: 1_pBS
Gene expression data from Caco-2 epithelial colonic tumor cell control sample.


title: CRTC1 n1

description:
Sample name: 2_CRTC1
Gene expression data from Caco-2 epithelial colonic tumor cell with CRTC1 overexpression.


title: Wild Type, leptin-stimulated, biological replicate 1

source_name: Wild Type, leptin-stimulated

value: 100ng leptin


title: CTRL n3

description:
Sample name: 5_pBS
Gene expression data from Caco-2 epithelial colonic tumor cell control sample.


title: C4-2 16h docetaxel (1nM) treated in full serum, replicate 2

city: Philadelphia

first: Karen

last: Knudsen

state: Pennsylvania

institute: Thomas Jefferson University - Kimmel Cancer Center

hyb_protocol: 5ug cDNA in 220ul hybridization cocktail was hybridized on the Affymetrix Human Gene 2.0 ST Array in a GeneChip Hybridization Oven 645. Target denaturation was performed at 99C for 2 minutes, 45C for 5min, followed by hybridization for 18h.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed with GenSpring 11.5 software. The expression data were RMA normalized, and filtered to remove low-expressing genes.
HuGene-2_0-st.pgf
HuGene-2_0-st.mps

label_protocol: 5ug cDNA was fragmanted and chemically labeled with biotin using the FL-Ovation cDNA biotin module (NuGen Technologies, Inc)

growth_protocol: Cells treated at ca. 80% confluency

extract_protocol: Standard Trizol RNA extraction, followed by cDNA amplification using the Ovation Pico WTA-system V2 RNA amplification system (NuGen Technologies, Inc)

treatment_protocol: 16h treatment with 1nM cabazitaxel, docetaxel, or control (EtOH)


title: Wild Type, leptin-stimulated, biological replicate 2


title: C4-2 16h cabazitaxel (1nM) treated in full serum, replicate 1


title: C4-2 16h cabazitaxel (1nM) treated in full serum, replicate 2


title: C4-2 16h docetaxel (1nM) treated in full serum, replicate 1


title: Wild Type, no leptin, biological replicate 2


title: Mutant, leptin-stimulated, biological replicate 2

source_name: Mutant, leptin-stimulated

value: Y1138L (STAT3-mutant) leptin receptor


title: Mutant, leptin-stimulated, biological replicate 3


title: C4-2 CTRL treated in full serum, replicate 2

value: CTRL treated in full serum


title: Wild Type, leptin-stimulated, biological replicate 3


title: Wild Type, no leptin, biological replicate 1


title: C4-2 CTRL treated in full serum, replicate 1


title: C4-2 16h docetaxel (1nM) treated in charcoal dextran treated serum, replicate 2


title: Mutant, no leptin, biological replicate 3

source_name: Mutant, no leptin


title: hiPSC-MSC-derived_putative dermal papilla substiture cells_rep2

first: Manabu

last: Ohyama

address: 6-20-2 Shinkawa Mitaka-shi

department: Department of Dermatology

institute: Kyorin University School of Medicine

description:
hiPSC-MSC-2 derived cells programed in retinoic acid, WNT, BMP and FGF activatiors
IpDPSC-2

hyb_protocol: 0.6 ug of Cy3-labelled 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 SurePrint G3 Human Gene Expression 8x60K v2 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B)

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. These data were normalized by 75th percentile normalisation by GeneSpring GX with default condition. The probes less than 100 in all six samples were filtered out. The full set of normalized data is available on the series record.

source_name: hiPSC-MSC-2 derived cells programed in retinoic acid, WNT, BMP and FGF activators

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug RNA using the Low Input Quick Amp Labelling Kit, one-color (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.

growth_protocol: Freshly microdissected human DP cells were cultured in PromoCell Follicle Papilla Cell Growth Medium (PromoCell, Heiderberg, Germany). hiPSCs-MSCs were cultured in Stempro MSC-SFM CTS (Life Technologies, Carlsbad, CA) supplemented with bFGF on a humanised substrate, CELLstart CTS (Life Technologies). After sorting, CD271+CD90+hiPSC-MSCs were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 0.01 mM all-trans retinoic acid (Sigma, St. louis, MO) (day 0-4). On day 4, induction medium was then changed to DMEM with 10%FBS, 20 ng/ ml bFGF (Peprotech, Rocky Hill, NJ), 200 ng/ ml human recombinant BMP2 (R&D Systems, Minneapolis, MN) and 1 μM 6-bromoindirubin-3'-oxime (Sigma) (day 4-9).

extract_protocol: Total RNA was harvested and purified using the RNeasy Mini (Qiagen, Hilden, Germany) following manufacutures instrcution. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For MSC induction, embryo bodies were formed  and kept for 2 days floating inhiPSC medium consisting of DMEM/Ham’s F12 medium (Sigma) containing 20% Knockout Serum Replacement (Life Technologies), 2 mM L-glutamine (Sigma), 1×10-4 M nonessential amino acids (Sigma), 1×10-4 M 2-mercaptoethanol (Sigma), 4 ng/ml FGF2 (Wako, Osaka, Japan), 0.5% penicillin and streptomycin (Life Technologies). Subsequently, they were cultured in Stempro MSC-SFM CTS (Life Technologies) on a humanised substrate, CELLstart CTS (Life Technologies) and cultured for a further 9-11 days as described in growth protocol. For sorting, hiPSC-MSC were detached, dissociated and incubated with mouse anti-human CD271 phycoerythrin-conjugated (Biolegend, San Diego, CA) and anti-human CD90 allophycocyanin-conjugated monoclonal antibodies (Biolegend) for 30 minutes. Single staining by each antibody was used as controls. Flow cytometric sorting was then performed on MoFlo XDP (Beckman Coulter, Brea, CA). The resultant cells were subject to dermal papilla induction culture as described in growth protocol.

value: dermis

value: female

value: 16y at reprogramming


title: dermal papilla_primarily_cultured_rep2

description:
dermal papilla, whole, microdissected from anagen hair follicles, cultured
hDP-2

value: anagen hair follicle

value: male


title: Mutant, no leptin, biological replicate 1


title: Mutant, no leptin, biological replicate 2


title: C4-2 16h cabazitaxel (1nM) treated in charcoal dextran treated serum, replicate 2


title: Mutant, leptin-stimulated, biological replicate 1


title: C4-2 CTRL treated in charcoal dextran treated serum, replicate 2


title: C4-2 16h cabazitaxel (1nM) treated in charcoal dextran treated serum, replicate 1


title: C4-2 16h docetaxel (1nM) treated in charcoal dextran treated serum, replicate 1


title: dermal papilla_primarily_cultured_rep1

description:
dermal papilla, whole, microdissected from anagen hair follicles, cultured
hDP-1


title: hiPSC-derived_MSC_rep1

description:
hiPSC (WD39) derived MSCs, CD271+CD90+ sorted fraction
hiPSC-MSC-1


title: hiPSC-MSC-derived_putative dermal papilla substiture cells_rep1

description:
hiPSC-MSC-1 derived cells programed in retinoic acid, WNT, BMP and FGF activatiors
ipDPSC-1

source_name: hiPSC-MSC-1 derived cells programed in retinoic acid, WNT, BMP and FGF activators


title: whole blood_injection of LTA from Bacillus_6h_rep3

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

hyb_protocol: The pre-hybridization of MRmiOA v2 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on MRmiOA v2 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 600-620 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: Among the probe triplicates, the median value were selected into signal normalization processed by R program (2.12.1).  We ﬁltered out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by quantile normalization within biological replicates and 75% media scaling normalization between treatments.

source_name: whole blood

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy5, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

extract_protocol: RNA extraction by RNeasy Protect Animal Blood Kit (QIAGEN Cat. no. 73224). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: C57BL/6 mice received intraperitoneal injections of 100 μg of LTA from different Gram-positive bacteria, including Bacillus subtilis (catalog no. L3265), Streptococcus faecalis (L4015), and Staphylococcus aureus (L2515) as well as LPS from different Gram-negative bacteria, including Escherichia coli serotype 026:B6 (L3755), Klebsiella pneumonia (L1519), Salmonella enterica serotype Enteritidis (L6761), Serratia marcescens (L6136), and Pseudomonas aeruginosa (L9143). The mice were killed 6 h and the whole blood samples were obtained for miRNA expression analysis using a miRNA array

tag: strain

value: LTA from Bacillus


title: whole blood_injection of LTA from Staphylococus_6h_rep1

value: LTA from Staphylococus


title: whole blood_injection of LTA from Staphylococus_6h_rep2


title: Infected_48h pi_Rep1

description: Gene expression data from JEV infected human microglial cells CHME13

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip Human PrimeView 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 Expression Console  using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

source_name: CHME3 cells grown on transwells - Infected With JEV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: CHME3 cells grown on 6-wells plate

extract_protocol: Total RNA prepared using Qiagen RNA extraction kit

treatment_protocol: Infected with an MOI of 5 pfu/cell of Japanese encephalitis virus (P20778 strain )

tag: infection

value: Japanese encephalitis virus

tag: time

value: Polarized cells


title: whole blood_injection of LTA from Bacillus_6h_rep2


title: whole blood_injection of LTA from Staphylococus_6h_rep3


title: LNCaP 16h docetaxel (1nM) treated in full serum, replicate 1

source_name: LNCaP

value: LNCaP


title: ftsZ Depletion Cells Induced 1hr Replicate 3

description: Biological replicate 3 of 3. FtsZ induced 1hr

source_name: ftsZ depletion

value: Induced for 1hr

source_name: pooled reference RNA

tag: sample type

value: Pooled RNA from mixture of the same amount of wt standards


title: LNCaP 16h docetaxel (1nM) treated in full serum, replicate 2


title: hiPSC-derived_MSC_rep2

description:
hiPSC (WD39) derived MSCs, CD271+CD90+ sorted fraction
hiPSC-MSC-2


title: LNCaP 16h cabazitaxel (1nM) treated in full serum, replicate 1


title: C4-2 CTRL treated in charcoal dextran treated serum, replicate 1


title: FEPS with daunorubicin replicate 1

description:
Gene expression data
FEPS.1+DAUNO

source_name: FEPS1 grown in RMPI 1640 medium with 10% FBS and 5% CO2 at 37oC, with 466nM daunorrubicin

value: FEPS

tag: cell line origin

value: Cell line derived from K562, selected for resistance to daunorubicin and with multidrug resentance phenotype, grown in the presence of daunorubicin

tag: agent

value: daunorubicin


title: Infected_48h pi_Rep2

description: Gene expression data from JEV infected human microglial cells CHME14


title: Uninfected_48h pi_Rep2

description: Gene expression data from JEV infected human microglial cells CHME12

source_name: CHME3 cells grown on transwells - Mock infected

value: uninfected


title: whole blood_injection of LTA from Bacillus_6h_rep1


title: LNCaP CTRL treated in full serum, replicate 1

value: CTRL treated in full serum


title: whole blood_injection of LTA from Streptococcus_6h_rep3

value: LTA from Streptococcus


title: whole blood_injection of LTA from Streptococcus_6h_rep1


title: whole blood_injection of LPS from Pseudomonas_6h_rep2

value: LPS from Pseudomonas


title: whole blood_injection of LPS from Pseudomonas_6h_rep3


title: whole blood_injection of LPS from Pseudomonas_6h_rep1


title: LNCaP 16h docetaxel (1nM) treated in charcoal dextran treated serum, replicate 1


title: Uninfected_48h pi_Rep1

description: Gene expression data from JEV infected human microglial cells CHME11


title: LNCaP 16h cabazitaxel (1nM) treated in charcoal dextran treated serum, replicate 2


title: LNCaP 16h docetaxel (1nM) treated in charcoal dextran treated serum, replicate 2


title: whole blood_injection of LPS from Serratia_6h_rep2

value: LPS from Serratia


title: whole blood_injection of LPS from Serratia_6h_rep1


title: Infected_24h pi_Rep2

description: Gene expression data from JEV infected human microglial cells CHME10


title: Infected_24h pi_Rep1

description: Gene expression data from JEV infected human microglial cells CHME9


title: whole blood_injection of LPS from Serratia_6h_rep3


title: LNCaP CTRL treated in charcoal dextran treated serum, replicate 2


title: LNCaP CTRL treated in charcoal dextran treated serum, replicate 1


title: Infected_6h pi_Rep2

description: Gene expression data from JEV infected human microglial cells CHME6

value: 6 h


title: LNCaP 16h cabazitaxel (1nM) treated in charcoal dextran treated serum, replicate 1


title: whole blood_injection of LTA from Streptococcus_6h_rep2


title: Uninfected_24h pi_Rep2

description: Gene expression data from JEV infected human microglial cells CHME8


title: Infected_6h pi_Rep1

description: Gene expression data from JEV infected human microglial cells CHME5


title: Uninfected_6h pi_Rep1

description: Gene expression data from JEV infected human microglial cells CHME3


title: whole blood_injection of LPS from Salmonella_6h_rep3

value: LPS from Salmonella


title: Uninfected_6h pi_Rep2

description: Gene expression data from JEV infected human microglial cells CHME4


title: whole blood_injection of LPS from Salmonella_6h_rep2


title: Uninfected_24h pi_Rep1

description: Gene expression data from JEV infected human microglial cells CHME7


title: whole blood_injection of LPS from Salmonella_6h_rep1


title: whole blood_injection of LPS from Klebsiella_6h_rep3

value: LPS from Klebsiella


title: whole blood_injection of LPS from Klebsiella_6h_rep2


title: LNCaP CTRL treated in full serum, replicate 2


title: whole blood_injection of LPS from Klebsiella_6h_rep1


title: whole blood_control_6h_rep3


title: whole blood_control_6h_rep1


title: whole blood_control_6h_rep2


title: Expression in colon mucosa 434

description: Normal colon mucosa sample

hyb_protocol: Fluidics Protocol FS450_0002

data_processing: The R Bioconductor affy package rma function was used to compute expression. The rma function performs probe specific correction of the PM probes using a model based on observed intensity being the sum of signal and noise, normalization of corrected PM probes using quantile normalization, and calculation of expression measure using median polish.

source_name: colon mucosa 434

label_protocol: Nugen Ovation Pico WTA System V2 /Encore Biotin Module

extract_protocol: Qiangen QIAzol

value: Male

value: Colon mucosa

tag: disease state

value: normal


title: Expression in colon mucosa 429

description: Normal colon mucosa sample

source_name: colon mucosa 429

tag: gender


title: Expression in colon mucosa 419

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 419

value: Female

value: Ulcerative colitis


title: 1676 control_-IL-7 24h_rep2

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

description: gene expression upon IL-7 withdrawal (24h)

hyb_protocol: 1.65 µg of each Cy3-labeled cRNA was fragmented and prepared for one-color based hybridisation (Gene Expression Hybridisation Kit, Agilent Technologies). cRNA samples were hybridized for 17 hours at 65°C on a Sureprint G3 Mouse Gene Expression Microarray (Agilent Technologies, AMADID 028005). Afterwards, microarrays were washed with increasing stringency using Geene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitril.

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner.

data_processing: Raw data were extracted from images using Feature Extraction 10.7.1.1 Software (Agilent Technologies). Data analysis was performed using the Subio software package (Subio, Japan).

source_name: mouse pre-B cell line, control vector, -IL7 24h, replicate 2

label_protocol: 100 ng total RNA per sample were used for an RT-IVT reaction. Total RNA was reverse transcribed into cDNA and then converted into labelled cRNA by in-vitro transcription (Low Input Quick-Amp Labeling Kit One-Color; Agilent Technologies) incorporating Cyanine-3-CTP according to the manufacturer's instructions. RNA absorbance ratio, cRNA concentration and Cy3 dye concentration were checked with the NanoDrop ND-1000 UV-VIS spectrophotometer. Furthermore, the quality of labeled non-fragmented cRNA was analyzed with the 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: 1676 cells were cultured in Iscove’s medium containing 7.5% FCS (Biochrom Superior), 100 U/ml penicillin, 100 U/ml streptomycin (PAN) and 50 µM 2-ME supplemented with excessive IL-7 obtained as a supernatant of IL-7-expressing J558L cells. Following infection with retroviral vectors, transduced cells were selected with puromycin at a concentration of 1 µg/ml for 3-4 days.

extract_protocol: Total RNA was prepared using the RNeasy RNA Purification kit (Qiagen) including on-column DNase digestion according to the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer (Peqlab) and integrity was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 1676 cells selected for expression of a control vector or a vector encoding hsa-miR-125b were cultured in excessive IL-7 or without IL-7 for 24 hours to induce pre-B cell differentiation.

value: pre-B cell

tag: genotype


title: Expression in colon mucosa 397

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 397


title: Expression in colon mucosa 432

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 432


title: the CD110+ cells from liver metastasis rep3 [CRC108-3LM]

city: Shanghai

first: Li

last: Qingquan

address: No.138，Yixueyuan Rd.

country: China

institute: fudan university

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: CRC108 xenograft

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

growth_protocol: 1×107 CRC102 or CRC108 cells were orthotopically implanted into 6-week old NOG mice and allowed to form primary tumors accompanied with liver metastases in 6 weeks, after which the CD110+ cells in primary tumors and liver metastases were sorted by flow cytometry.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: male

value: liver

tag: tumor stage

value: IV stage


title: the CD110+ cells from primary tumor rep3 [CRC108-3PT]

description: replicate 3

tag: tissue

value: colon


title: 1676 miR-125b_-IL-7 24h_rep2

source_name: mouse pre-B cell line, expression of hsa-miR-125b-1, -IL7 24h, replicate 2


title: Testis_8week_rep2

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

hyb_protocol: Hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Microarrays were hybridized at 65°C for 17 hours in agilent’s SureHyb Hybridization Chambers.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with Wash buffer 2 (Agilent) at 37°C, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (part number 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 Agilent Feature Extraction Software  (version 10.5.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The resulting text files extracted from Agilent Feature Extraction Software were imported into the Agilent GeneSpring GX software (version 11.0) for quantile normalization and background correction.

source_name: Testis, 8week, replicate 2

label_protocol: Double-strand cDNA was synthetized from RNA with oligo dT primer using Superscript Double-Strand Synthesis Kit (Invitrogen, 11917-020) following the manufacturers’s instructions. cDNA was labeled with Cy3 using the Quick Amp labeling kit (Agilent) according to the protocols provided by the manufacturers. Labeled cDNA quantification and quality were assessed using NanoDrop-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: Mice used in this study are specific pathogen free (SPF), and are conducted in accordance with the National Research Council Guide for Care and Use of Laboratory Animals [SYXK (Shanghai 2007-0025)]

extract_protocol: RNA derived from mouse testis was purified using Trizol Reagent (Invitrogen) and treated with DNase I (Fermentas), according to the protocols provided by the manufacturers. The quantification and quality of purified total RNA samples were assessed by NanoDrop ND-1000 Spectrophotometer(Thermo Scientific). RNA integrity and genomic DNA contamination were examined by denaturing agarose gel electrophoresis.

value: testis

tag: developmental stage

value: 8 week postpartum


title: Expression in colon mucosa 395

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 395

tag: age


title: the CD110+ cells from primary tumor rep2 [CRC108-2PT]

description: replicate 2


title: the CD110+ cells from liver metastasis rep2 [CRC108-2LM]

description: replicate 2


title: Expression in colon mucosa 206

description: Normal colon mucosa sample

source_name: colon mucosa 206


title: the CD110+ cells from liver metastasis rep1 [CRC108-1LM]

description: replicate 1


title: Expression in colon mucosa 416

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa 416


title: the CD110+ cells from primary tumor rep1 [CRC108-1PT]

description: replicate 1


title: 1676 miR-125b_+IL-7_rep1

description: gene expression in the presence of IL-7

source_name: mouse pre-B cell line, expression of hsa-miR-125b-1, +IL7, replicate 1


title: Testis_8week_rep3

source_name: Testis, 8week, replicate 3


title: Testis_8week_rep1

source_name: Testis, 8week, replicate 1


title: 1676 miR-125b_+IL-7_rep2

description: gene expression in the presence of IL-7

source_name: mouse pre-B cell line, expression of hsa-miR-125b-1, +IL7, replicate 2


title: 1676 control_-IL-7 24h_rep1

source_name: mouse pre-B cell line, control vector, -IL7 24h, replicate 1


title: 1676 miR-125b_-IL-7 24h_rep1

source_name: mouse pre-B cell line, expression of hsa-miR-125b-1, -IL7 24h, replicate 1


title: the CD110+ cells from liver metastasis rep3 [CRC102-3LM]

description: replicate 3

source_name: CRC102 xenograft

value: III stage


title: Testis_6day_rep2

source_name: Testis, 6dpp, replicate 2

value: 6 day postpartum


title: Testis_6day_rep1

source_name: Testis, 6dpp, replicate 1


title: the CD110+ cells from primary tumor rep3 [CRC102-3PT]

description: replicate 3


title: the CD110+ cells from liver metastasis rep2 [CRC102-2LM]

description: replicate 2


title: the CD110+ cells from liver metastasis rep1 [CRC102-1LM]

description: replicate 1


title: the CD110+ cells from primary tumor rep2 [CRC102-2PT]

description: replicate 2


title: mated_PfXPm_SelRep2_BioRep3

city: Uppsala

first: Göran

last: Arnqvist

address: Norbyvägen 18D

department: Ecology and Genetics

country: Sweden

institute: Uppsala University

hyb_protocol: Hybridisation and washing was carried out according to the Low Input Quick Amp protocol mentioned above (washes with acetonitrile and drying and stabilisation solution were NOT carried out).

scan_protocol: Microarrays were scanned on an Agilent Technologies DNA Microarray Scanner (with Surescan High-Resolution Technology) at a resolution of 5um, PMT was 100% and 20 bit TIFF images were generated. Data was extracted using Agilent Feature extraction version 10.5.5.1.

data_processing: Raw signal intensities were background corrected with method normexp and normalised with method quantile, within limma package in Bioconductor.

organism: Drosophila pseudoobscura

source_name: Ployandrous female from selection replicate line 2 mated to polyandrous male from the same line, biological replicate 3

label_protocol: Low Input Quick Amp Labelling kit for One-Colour Microarray-Based Gene Expression Analysis (Agilent; protocol version 6.5, May 2010). Used 50ng of total RNA in each labelling reaction.

extract_protocol: Trizol Plus RNA purification system with on-column Purelink DNase treatment (Invitrogen, now Life Technologies). Total RNA was QC'd by analysis on the Agilent Bioanalyser (RNA Nano chip) and sample concentrations and A260/280 and A260/230 ratios were obtained using a Nanodrop.

tag: female state

value: mated

tag: selection regime_female

value: P

tag: selection regime_mate

tag: selection line replicate

value: whole body


title: OldAdult_LyoVec_only_6hrs OA_8

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
Sample ID: E763
Sample name: 7018861098_J
OldAdult_LyoVec_only_6hrs

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to HumanHT-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC). The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the limma from the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

source_name: PBMC, old adult, LyoVec_only, 6h

label_protocol: Labeling was done with Ambion's Illumina kit as specified by Illumina's direct hybridization protocol.

growth_protocol: Gene expression was analyzed directly ex vivo.

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment. Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system. With each batch of samples, a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: Total PBMCs isolated from adults and old subjects were plated in triplicate at 100,000 cells/well in 96-well U-bottom plates. TLR and RIG-I agonists were added at the following concentrations: LPS-TLR4 (0.5 µg/ml) or CLO97-TLR7/8 (0.5 µg/ml) or poly I:C/Lyovec-RIGI/MDA5 (2 µg/ml) or 5’-pppRNA/Lyovec-RIG-I (400 ng/ml). PBMCs cultured in medium alone were used as a control for LPS and CLO97. Stimulation by poly I:C and 5’-pppRNA required the use of a cationic transfection agent LyoVec (InvivoGen), so medium plus Lyovec alone was used as a control for these two agonists. PBMCs were cultured for 6 and 24 hrs at 37oC in a 5% CO2-humidified environment.

tag: donor

tag: age class

value: old adult

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment


title: mated_PfXPm_SelRep2_BioRep2

source_name: Ployandrous female from selection replicate line 2 mated to polyandrous male from the same line, biological replicate 2


title: mated_MfXPm_SelRep2_BioRep2

source_name: Monogamous female from selection replicate line 2 mated to polyandrous male from the same line, biological replicate 2

value: M


title: mated_MfXPm_SelRep2_BioRep1

source_name: Monogamous female from selection replicate line 2 mated to polyandrous male from the same line, biological replicate 1

value: Female


title: OldAdult_LyoVec_only_24hrs OA_8

description:
Sample ID: E766
Sample name: 6898350039_K
OldAdult_LyoVec_only_24hrs

source_name: PBMC, old adult, LyoVec_only, 24h

tag: time


title: mated_PfXPm_SelRep2_BioRep1

source_name: Ployandrous female from selection replicate line 2 mated to polyandrous male from the same line, biological replicate 1


title: OldAdult_Rig_I_24hrs OA_8

description:
Sample ID: E749
Sample name: 7018861099_G
OldAdult_Rig_I_24hrs

source_name: PBMC, old adult, Rig I, 24h

value: Rig I


title: OldAdult_No_treatment_24hrs OA_8

description:
Sample ID: E760
Sample name: 6898350039_L
OldAdult_No_treatment_24hrs

source_name: PBMC, old adult, NoTx, 24h

value: NoTx


title: virgin_Pf_SelRep2_BioRep1

source_name: Polyandrous virgin female from selection replicate line 2, biological replicate 1

value: virgin


title: mated_MfXPm_SelRep2_BioRep3

source_name: Monogamous female from selection replicate line 2 mated to polyandrous male from the same line, biological replicate 3


title: OldAdult_LPS_6hrs OA_8

description:
Sample ID: E739
Sample name: 6898350005_H
OldAdult_LPS_6hrs

source_name: PBMC, old adult, LPS, 6h

value: LPS


title: virgin_Pf_SelRep1_BioRep1

source_name: Polyandrous virgin female from selection replicate line 1, biological replicate 1


title: virgin_Pf_SelRep1_BioRep2

source_name: Polyandrous virgin female from selection replicate line 1, biological replicate 2


title: OldAdult_CLO_97_24hrs OA_8

description:
Sample ID: E730
Sample name: 6898350039_I
OldAdult_CLO_97_24hrs

source_name: PBMC, old adult, CLO_97, 24h


title: OldAdult_Poly_IC_24hrs OA_8

description:
Sample ID: E754
Sample name: 7018861084_D
OldAdult_Poly_IC_24hrs

source_name: PBMC, old adult, PolyIC, 24h

value: PolyIC


title: OldAdult_Poly_IC_6hrs OA_8

description:
Sample ID: E751
Sample name: 6898481077_G
OldAdult_Poly_IC_6hrs

source_name: PBMC, old adult, PolyIC, 6h


title: virgin_Pf_SelRep1_BioRep3

source_name: Polyandrous virgin female from selection replicate line 1, biological replicate 3


title: virgin_Pf_SelRep2_BioRep3

source_name: Polyandrous virgin female from selection replicate line 2, biological replicate 3


title: mated_MfXPm_SelRep1_BioRep3

source_name: Monogamous female from selection replicate line 1 mated to polyandrous male from the same line, biological replicate 3


title: the CD110+ cells from primary tumor rep1 [CRC102-1PT]

description: replicate 1

source_name: CRC102 xenograft

value: male

value: colon


title: mated_MfXPm_SelRep1_BioRep2

source_name: Monogamous female from selection replicate line 1 mated to polyandrous male from the same line, biological replicate 2


title: OldAdult_LPS_24hrs OA_8

description:
Sample ID: E742
Sample name: 8118927047_L
OldAdult_LPS_24hrs

source_name: PBMC, old adult, LPS, 24h


title: mated_MfXPm_SelRep1_BioRep1

source_name: Monogamous female from selection replicate line 1 mated to polyandrous male from the same line, biological replicate 1


title: OldAdult_LyoVec_only_6hrs OA_7

description:
Sample ID: E715
Sample name: 7018861051_C
OldAdult_LyoVec_only_6hrs

source_name: PBMC, old adult, LyoVec_only, 6h


title: OldAdult_CLO_97_6hrs OA_8

description:
Sample ID: E727
Sample name: 6991010093_B
OldAdult_CLO_97_6hrs

source_name: PBMC, old adult, CLO_97, 6h


title: LNCaP 16h cabazitaxel (1nM) treated in full serum, replicate 2

source_name: LNCaP

tag: cell line

value: LNCaP


title: virgin_Pf_SelRep2_BioRep2

source_name: Polyandrous virgin female from selection replicate line 2, biological replicate 2


title: virgin_Mf_SelRep1_BioRep2

source_name: Monogamous virgin female from selection replicate line 1, biological replicate 2


title: mated_PfXMm_SelRep2_BioRep3

source_name: Ployandrous female from selection replicate line 2 mated to monogamous male from the same line, biological replicate 3


title: mated_PfXMm_SelRep1_BioRep3

source_name: Ployandrous female from selection replicate line 1 mated to monogamous male from the same line, biological replicate 3


title: OldAdult_Rig_I_24hrs OA_7

description:
Sample ID: E701
Sample name: 7018861087_A
OldAdult_Rig_I_24hrs

source_name: PBMC, old adult, Rig I, 24h


title: OldAdult_Poly_IC_6hrs OA_7

description:
Sample ID: E703
Sample name: 7018861087_D
OldAdult_Poly_IC_6hrs


title: mated_PfXMm_SelRep1_BioRep2

source_name: Ployandrous female from selection replicate line 1 mated to monogamous male from the same line, biological replicate 2


title: virgin_Mf_SelRep1_BioRep3

source_name: Monogamous virgin female from selection replicate line 1, biological replicate 3


title: OldAdult_LyoVec_only_24hrs OA_6

description:
Sample ID: E670
Sample name: 7018861098_B
OldAdult_LyoVec_only_24hrs

source_name: PBMC, old adult, LyoVec_only, 24h


title: mated_PfXMm_SelRep2_BioRep1

source_name: Ployandrous female from selection replicate line 2 mated to monogamous male from the same line, biological replicate 1


title: mated_PfXMm_SelRep1_BioRep1

source_name: Ployandrous female from selection replicate line 1 mated to monogamous male from the same line, biological replicate 1


title: mated_PfXMm_SelRep2_BioRep2

source_name: Ployandrous female from selection replicate line 2 mated to monogamous male from the same line, biological replicate 2


title: virgin_Mf_SelRep1_BioRep1

source_name: Monogamous virgin female from selection replicate line 1, biological replicate 1


title: OldAdult_LPS_24hrs OA_7

description:
Sample ID: E694
Sample name: 6898368101_A
OldAdult_LPS_24hrs

source_name: PBMC, old adult, LPS, 24h


title: mated_MfXMm_SelRep2_BioRep2

source_name: Monogamous female from selection replicate line 2 mated to monogamous male from the same line, biological replicate 2


title: OldAdult_CLO_97_6hrs OA_7

description:
Sample ID: E679
Sample name: 6991010093_J
OldAdult_CLO_97_6hrs


title: OldAdult_No_treatment_24hrs OA_6

description:
Sample ID: E664
Sample name: 6991010102_K
OldAdult_No_treatment_24hrs

source_name: PBMC, old adult, NoTx, 24h


title: OldAdult_LPS_6hrs OA_7

description:
Sample ID: E691
Sample name: 6991010093_I
OldAdult_LPS_6hrs

source_name: PBMC, old adult, LPS, 6h


title: OldAdult_Poly_IC_6hrs OA_6

description:
Sample ID: E655
Sample name: 7018879019_L
OldAdult_Poly_IC_6hrs

source_name: PBMC, old adult, PolyIC, 6h


title: mated_MfXMm_SelRep2_BioRep1

source_name: Monogamous female from selection replicate line 2 mated to monogamous male from the same line, biological replicate 1


title: mated_PfXPm_SelRep1_BioRep3

source_name: Ployandrous female from selection replicate line 1 mated to polyandrous male from the same line, biological replicate 3


title: OldAdult_No_treatment_6hrs OA_6

description:
Sample ID: E661
Sample name: 6898481077_D
OldAdult_No_treatment_6hrs

source_name: PBMC, old adult, NoTx, 6h


title: virgin_Mf_SelRep2_BioRep3

source_name: Monogamous virgin female from selection replicate line 2, biological replicate 3


title: mated_PfXPm_SelRep1_BioRep2

source_name: Ployandrous female from selection replicate line 1 mated to polyandrous male from the same line, biological replicate 2


title: mated_MfXMm_SelRep2_BioRep3

source_name: Monogamous female from selection replicate line 2 mated to monogamous male from the same line, biological replicate 3


title: OldAdult_LyoVec_only_6hrs OA_6

description:
Sample ID: E667
Sample name: 6898368101_L
OldAdult_LyoVec_only_6hrs

source_name: PBMC, old adult, LyoVec_only, 6h


title: mated_PfXPm_SelRep1_BioRep1

source_name: Ployandrous female from selection replicate line 1 mated to polyandrous male from the same line, biological replicate 1


title: virgin_Mf_SelRep2_BioRep1

source_name: Monogamous virgin female from selection replicate line 2, biological replicate 1


title: OldAdult_No_treatment_6hrs OA_7

description:
Sample ID: E709
Sample name: 7018861084_I
OldAdult_No_treatment_6hrs


title: mated_MfXMm_SelRep1_BioRep2

source_name: Monogamous female from selection replicate line 1 mated to monogamous male from the same line, biological replicate 2


title: OldAdult_Rig_I_24hrs OA_6

description:
Sample ID: E653
Sample name: 7018861099_K
OldAdult_Rig_I_24hrs

source_name: PBMC, old adult, Rig I, 24h


title: OldAdult_Rig_I_6hrs OA_6

description:
Sample ID: E650
Sample name: 8118927047_G
OldAdult_Rig_I_6hrs

source_name: PBMC, old adult, Rig I, 6h


title: OldAdult_No_treatment_6hrs OA_5

description:
Sample ID: E613
Sample name: 7018861099_L
OldAdult_No_treatment_6hrs


title: virgin_Mf_SelRep2_BioRep2

source_name: Monogamous virgin female from selection replicate line 2, biological replicate 2


title: mated_MfXMm_SelRep1_BioRep3

source_name: Monogamous female from selection replicate line 1 mated to monogamous male from the same line, biological replicate 3


title: OldAdult_Poly_IC_24hrs OA_6

description:
Sample ID: E658
Sample name: 6991010093_D
OldAdult_Poly_IC_24hrs

source_name: PBMC, old adult, PolyIC, 24h


title: OldAdult_Rig_I_6hrs OA_7

description:
Sample ID: E698
Sample name: 7018861087_B
OldAdult_Rig_I_6hrs


title: OldAdult_LPS_6hrs OA_6

description:
Sample ID: E643
Sample name: 7018861087_E
OldAdult_LPS_6hrs

source_name: PBMC, old adult, LPS, 6h


title: OldAdult_CLO_97_24hrs OA_6

description:
Sample ID: E634
Sample name: 7018879026_H
OldAdult_CLO_97_24hrs

source_name: PBMC, old adult, CLO_97, 24h


title: Testis_6day_rep3

source_name: Testis, 6dpp, replicate 3

tag: strain

value: testis


title: mated_MfXMm_SelRep1_BioRep1

source_name: Monogamous female from selection replicate line 1 mated to monogamous male from the same line, biological replicate 1

tag: gender


title: OldAdult_LyoVec_only_24hrs OA_5

description:
Sample ID: E622
Sample name: 6898481080_G
OldAdult_LyoVec_only_24hrs

source_name: PBMC, old adult, LyoVec_only, 24h


title: OldAdult_CLO_97_6hrs OA_6

description:
Sample ID: E631
Sample name: 6898481077_F
OldAdult_CLO_97_6hrs

source_name: PBMC, old adult, CLO_97, 6h


title: OldAdult_No_treatment_24hrs OA_5

description:
Sample ID: E616
Sample name: 7018861084_F
OldAdult_No_treatment_24hrs

source_name: PBMC, old adult, NoTx, 24h


title: OldAdult_Poly_IC_24hrs OA_5

description:
Sample ID: E610
Sample name: 6898481077_A
OldAdult_Poly_IC_24hrs


title: OldAdult_Poly_IC_6hrs OA_5

description:
Sample ID: E607
Sample name: 6898350039_H
OldAdult_Poly_IC_6hrs

source_name: PBMC, old adult, PolyIC, 6h


title: OldAdult_LPS_24hrs OA_6

description:
Sample ID: E646
Sample name: 7018861084_A
OldAdult_LPS_24hrs

source_name: PBMC, old adult, LPS, 24h


title: K3li3

city: Heidelberg

first: Doreen

last: Heckmann

country: Germany

institute: DKFZ

hyb_protocol: Standard affymetrix GeneTitan hybridization protocol for GeneChip Human Genome U219 array plates

scan_protocol: Scanning was performed by GeneTitan Instrument. Affymetrix GeneChip Command Console 3.1 was used to control the process and to summarize probe cell intensity data.

data_processing: The files containing a single intensity value for each probe region delineated by a grid on each array image were imported into Partek Genomics Suite (version 6.6, Partek, St. Louis, MO) for probe set summarization and statistical analysis. Model based Robust Multichip Analysis was performed.

source_name: skin fibroblasts, healthy control

label_protocol: Affymetrix standard 3' labelling protocol, GeneChip IVT Express Kit (Part no. 901229)

growth_protocol: Skin biopsies of both arms were obtained from four SRS patients and three healthy volunteers. Fibroblast cultures were cultivated in RPMI (Invitrogen, Karlsruhe, Germany), supplemented with 10% fetal calf serum (FCS; Biochrom, Berlin, Germany), 100 units/ml penicillin/streptomycin (Biochrom), and incubated in a 37°C humidified atmosphere containing 5% CO2.

extract_protocol: RNA was isolated from clonal fibroblasts using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).

tag: diagnosis

value: Healthy control

value: skin fibroblasts

tag: methylation

value: Cnormo


title: K1li5


title: S1sh12

source_name: skin fibroblasts, SRS patient

value: Silver-Russell syndrome

value: SRShypo


title: S3lo9


title: S5lo9

value: SRSnormo


title: S5sh11


title: S1sh9


title: K3re12


title: OldAdult_Rig_I_24hrs OA_5

description:
Sample ID: E604
Sample name: 7018861087_J
OldAdult_Rig_I_24hrs

value: old adult

value: peripheral blood mononuclear cells (PBMCs)


title: OldAdult_LyoVec_only_6hrs OA_5

description:
Sample ID: E619
Sample name: 6898481080_H
OldAdult_LyoVec_only_6hrs

source_name: PBMC, old adult, LyoVec_only, 6h


title: S2sh1


title: K2li17


title: S3sh19


title: OldAdult_No_treatment_24hrs OA_4

description:
Sample ID: E568
Sample name: 6990990031_D
OldAdult_No_treatment_24hrs


title: OldAdult_Poly_IC_24hrs OA_4

description:
Sample ID: E562
Sample name: 7018879026_L
OldAdult_Poly_IC_24hrs


title: OldAdult_CLO_97_6hrs OA_5

description:
Sample ID: E583
Sample name: 7018879019_E
OldAdult_CLO_97_6hrs


title: OldAdult_LPS_6hrs OA_5

description:
Sample ID: E595
Sample name: 6898368101_K
OldAdult_LPS_6hrs


title: OldAdult_No_treatment_6hrs OA_4

description:
Sample ID: E565
Sample name: 7018879026_G
OldAdult_No_treatment_6hrs

source_name: PBMC, old adult, NoTx, 6h


title: OldAdult_Poly_IC_6hrs OA_4

description:
Sample ID: E559
Sample name: 6991010102_B
OldAdult_Poly_IC_6hrs


title: S1sh8


title: OldAdult_CLO_97_24hrs OA_5

description:
Sample ID: E586
Sample name: 7018879026_F
OldAdult_CLO_97_24hrs


title: S1sh6


title: OldAdult_LPS_6hrs OA_4

description:
Sample ID: E547
Sample name: 7018879019_B
OldAdult_LPS_6hrs


title: OldAdult_Rig_I_6hrs OA_4

description:
Sample ID: E553
Sample name: 7018861087_F
OldAdult_Rig_I_6hrs

source_name: PBMC, old adult, Rig I, 6h

value: Rig I


title: OldAdult_Rig_I_24hrs OA_4

description:
Sample ID: E557
Sample name: 7018861051_G
OldAdult_Rig_I_24hrs

source_name: PBMC, old adult, Rig I, 24h


title: OldAdult_LPS_24hrs OA_4

description:
Sample ID: E550
Sample name: 6898481077_L
OldAdult_LPS_24hrs


title: S5lo10


title: S2lo7


title: OldAdult_LyoVec_only_24hrs OA_4

description:
Sample ID: E574
Sample name: 6898368101_B
OldAdult_LyoVec_only_24hrs


title: S2lo1


title: OldAdult_Poly_IC_6hrs OA_3

description:
Sample ID: E511
Sample name: 7018861098_K
OldAdult_Poly_IC_6hrs


title: OldAdult_LyoVec_only_6hrs OA_3

description:
Sample ID: E523
Sample name: 6990990031_K
OldAdult_LyoVec_only_6hrs


title: OldAdult_LyoVec_only_24hrs OA_3

description:
Sample ID: E526
Sample name: 6898481080_B
OldAdult_LyoVec_only_24hrs


title: Chlamydomonas sulfur stress T0-T4 rep 2

city: Bielefeld

first: Jörg

last: Toepel

address: Universitätsstrasse 27

department: Biology

institute: University of Bielefeld

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (10.7.3.1; Agilent).

data_processing: Agilent Feature Extraction Software (10.7.3.1) was used for background subtraction and EMMA2 was used for LOWESS normalization and significance tests.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii

label_protocol: 1 µg of total RNA were labeld according to the agilent quick amplification labeling kit

growth_protocol: TAP media with or without sulfur in sealed bioreactor

extract_protocol: Total RNA extracted using Phenol Chloroform extraction

tag: age (h)

tag: tissue

value: cells


title: OldAdult_No_treatment_24hrs OA_3

description:
Sample ID: E520
Sample name: 6898368101_J
OldAdult_No_treatment_24hrs

value: NoTx


title: Chlamydomonas sulfur stress T0-T3 rep 2


title: C. glutamicum W.T_Furfural 20 mM_rep2

city: Seoul

first: Han

middle: Min

last: Woo

address: Hwarangno 14-gil 5, Seongbuk-gu

department: Clean Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology

description: 0 vs 20 set2

hyb_protocol: After checking labeling efficiency, cyanine 3-labeled and cyanine 5-labeled cRNA target were combined and fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Cryptococcus neoformans 3X20K microarray (MYcroarray.com, USA). The arrays hybridized at 57oC for 17 h using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were visualized with Axon GenePix 4000B Scanner (Axon Instrument, CA)

data_processing: The data quantification was performed using GenePix Pro 6.0 (Axon Instrument, CA). All data normalization and the selection of fold changes were performed  using GeneSpring 7.3.1 (Agilent Technology). Intensity-dependent (Lowess)  normalization was performed, in which the ratio was reduced to the residual  of the Lowess fit for the intensity-versus-ratio curve. The averages of the  normalized ratios were calculated by dividing the average normalized signal channel intensity by the average normalized control channel intensity.

organism: Corynebacterium glutamicum ATCC 13032

source_name: C. glutamicum WT_furfural 0 mM

label_protocol: the synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, two color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2 ug total RNA was mixed with WT primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours.

growth_protocol: CgXII medium without furfural and with furfural stresses (each 6.5 mM, 13 mM, and 20 mM)

extract_protocol: Total RNA was extracted by using TRIzol (Invitrogen, Carlsbad, CA), according to the manufacturer’s protocol.

tag: genotype/variation

value: wild type

tag: culture medium

value: CgXII medium without furfural (control)

tag: culture density/stage

source_name: C. glutamicum WT_furfural 20 mM

value: CgXII medium with 20 mM Furfural


title: Chlamydomonas sulfur stress T0-T2 rep 2


title: Chlamydomonas sulfur stress T0-T4 rep 3


title: OldAdult_CLO_97_24hrs OA_4

description:
Sample ID: E538
Sample name: 6898481080_A
OldAdult_CLO_97_24hrs

source_name: PBMC, old adult, CLO_97, 24h


title: Chlamydomonas sulfur stress T0-T2 rep 3


title: Chlamydomonas sulfur stress T0-T4 rep 1


title: OldAdult_CLO_97_6hrs OA_4

description:
Sample ID: E535
Sample name: 6898350039_F
OldAdult_CLO_97_6hrs


title: Chlamydomonas sulfur stress T0-T3 rep 3


title: Chlamydomonas sulfur stress T0-T2 rep 1


title: Chlamydomonas sulfur stress T0-T1 rep 2


title: OldAdult_LyoVec_only_24hrs OA_2

description:
Sample ID: E478
Sample name: 6898368101_G
OldAdult_LyoVec_only_24hrs


title: OldAdult_No_treatment_6hrs OA_3

description:
Sample ID: E517
Sample name: 7018861099_E
OldAdult_No_treatment_6hrs


title: Chlamydomonas sulfur stress T0-T1 rep 3


title: OldAdult_Rig_I_24hrs OA_3

description:
Sample ID: E509
Sample name: 8118927047_B
OldAdult_Rig_I_24hrs


title: Chlamydomonas sulfur stress T0-T1 rep 1


title: OldAdult_CLO_97_24hrs OA_3

description:
Sample ID: E490
Sample name: 6898481077_H
OldAdult_CLO_97_24hrs


title: OldAdult_LyoVec_only_6hrs OA_2

description:
Sample ID: E475
Sample name: 6991010102_G
OldAdult_LyoVec_only_6hrs


title: OldAdult_Rig_I_6hrs OA_3

description:
Sample ID: E506
Sample name: 7018861051_E
OldAdult_Rig_I_6hrs


title: OldAdult_LPS_6hrs OA_3

description:
Sample ID: E499
Sample name: 6898350005_C
OldAdult_LPS_6hrs

source_name: PBMC, old adult, LPS, 6h

value: LPS


title: OldAdult_Poly_IC_24hrs OA_3

description:
Sample ID: E514
Sample name: 6990990031_L
OldAdult_Poly_IC_24hrs

source_name: PBMC, old adult, PolyIC, 24h

value: PolyIC


title: Chlamydomonas sulfur stress T0-T3 rep 1


title: OldAdult_CLO_97_6hrs OA_3

description:
Sample ID: E487
Sample name: 6898481080_I
OldAdult_CLO_97_6hrs


title: C. glutamicum W.T_Furfural 20 mM_rep1

description: 0 vs 20 set1


title: OldAdult_No_treatment_24hrs OA_2

description:
Sample ID: E472
Sample name: 7018879019_J
OldAdult_No_treatment_24hrs


title: C. glutamicum W.T_Furfural 13 mM_rep1

description: 0 vs 13 set1

source_name: C. glutamicum WT_furfural 13 mM

value: CgXII medium with 13 mM Furfural


title: C. glutamicum W.T_Furfural 6.5 mM_rep2

description: 0 vs 6.5 set2

source_name: C. glutamicum WT_furfural 6.5 mM

value: CgXII medium with 6.5 mM Furfural


title: C. glutamicum W.T_Furfural 13 mM_rep2

description: 0 vs 13 set2


title: OldAdult_Poly_IC_24hrs OA_2

description:
Sample ID: E466
Sample name: 7018879019_C
OldAdult_Poly_IC_24hrs


title: OldAdult_Rig_I_6hrs OA_2

description:
Sample ID: E458
Sample name: 7018861051_I
OldAdult_Rig_I_6hrs


title: OldAdult_LPS_6hrs OA_2

description:
Sample ID: E451
Sample name: 6991010102_F
OldAdult_LPS_6hrs


title: C. glutamicum W.T_Furfural 6.5 mM_rep1

description: 0 vs 6.5 set1


title: OldAdult_Rig_I_24hrs OA_2

description:
Sample ID: E461
Sample name: 8118927047_H
OldAdult_Rig_I_24hrs


title: OldAdult_No_treatment_6hrs OA_2

description:
Sample ID: E469
Sample name: 7018861051_D
OldAdult_No_treatment_6hrs


title: OldAdult_Poly_IC_6hrs OA_2

description:
Sample ID: E463
Sample name: 7018879019_K
OldAdult_Poly_IC_6hrs


title: OldAdult_No_treatment_24hrs OA_1

description:
Sample ID: E424
Sample name: 7018861084_H
OldAdult_No_treatment_24hrs

source_name: PBMC, old adult, NoTx, 24h


title: OldAdult_LyoVec_only_6hrs OA_1

description:
Sample ID: E427
Sample name: 6898481077_E
OldAdult_LyoVec_only_6hrs


title: OldAdult_LPS_24hrs OA_2

description:
Sample ID: E454
Sample name: 6898350039_E
OldAdult_LPS_24hrs


title: OldAdult_LyoVec_only_24hrs OA_1

description:
Sample ID: E430
Sample name: 6898350005_E
OldAdult_LyoVec_only_24hrs

source_name: PBMC, old adult, LyoVec_only, 24h


title: OldAdult_CLO_97_6hrs OA_2

description:
Sample ID: E439
Sample name: 7018879026_B
OldAdult_CLO_97_6hrs

source_name: PBMC, old adult, CLO_97, 6h


title: OldAdult_No_treatment_6hrs OA_1

description:
Sample ID: E421
Sample name: 7018861051_K
OldAdult_No_treatment_6hrs


title: OldAdult_LyoVec_only_6hrs OA_4

description:
Sample ID: E571
Sample name: 8118927047_E
OldAdult_LyoVec_only_6hrs


title: OldAdult_CLO_97_24hrs OA_2

description:
Sample ID: E442
Sample name: 6898350005_I
OldAdult_CLO_97_24hrs


title: OldAdult_Poly_IC_6hrs OA_1

description:
Sample ID: E415
Sample name: 7018879026_I
OldAdult_Poly_IC_6hrs

source_name: PBMC, old adult, PolyIC, 6h


title: OldAdult_Rig_I_24hrs OA_1

description:
Sample ID: E413
Sample name: 8118927047_K
OldAdult_Rig_I_24hrs


title: OldAdult_LPS_24hrs OA_1

description:
Sample ID: E406
Sample name: 8118927047_J
OldAdult_LPS_24hrs

source_name: PBMC, old adult, LPS, 24h


title: OldAdult_LPS_6hrs OA_1

description:
Sample ID: E403
Sample name: 6898368101_C
OldAdult_LPS_6hrs


title: OldAdult_CLO_97_24hrs OA_1

description:
Sample ID: E394
Sample name: 6991010102_E
OldAdult_CLO_97_24hrs


title: 9247377118_R04C02

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute

description: technical replicate: 9247377118_R06C02

hyb_protocol: Infinium Methylation Assay according to manufacturers protocol (Illumina)

scan_protocol: iScan system

data_processing: idat files processed in Minfi normalized using the stratified quantile normalization method. Sex probes removed, cross hybridizing probes removed, poor quality probes removed, SNP probes (MAF < 0.05 at extension site) removed

label: Cy5 and Cy3

source_name: gDNA from normal PBMC

label_protocol: Cy5 and Cy3

growth_protocol: untouched cells rested for 48 hours in RPMI media (serum free)

extract_protocol: DNA purified using Qiagen All prep column extraction method

value: FEMALE

tag: phenotype

tag: challenge outcome

value: allergic


title: OldAdult_Rig_I_6hrs OA_1

description:
Sample ID: E410
Sample name: 7018861099_D
OldAdult_Rig_I_6hrs

tag: donor


title: YoungAdult_LyoVec_only_6hrs YA_8

description:
Sample ID: E379
Sample name: 6991010093_C
YoungAdult_LyoVec_only_6hrs

source_name: PBMC, young adult, LyoVec_only, 6h

tag: age class

value: young adult


title: NPCs_from_CCTL14_p22_Ctrl

city: Brno

first: Marek

last: Mraz

address: Cernopolni 9

department: Dept. Hematology and Oncology

country: Czech Republic

institute: University Hospital Brno

hyb_protocol: as described in PMID: 18274534

scan_protocol: as described in PMID: 18274534

data_processing: Average values of two replicate spots of each miRNA on the array were background subtracted, processed, and normalized by the Limma & Marray package in the R Bioconductor in “R” environment.

label_protocol: as described in PMID: 18274534

growth_protocol: To induce neural differentiation, we utilized a protocol based on embryoid body (EB) formation with simultaneous all-trans-retinoic acid (RA) treatment. Colonies of hESCs were transferred to a non-adherent cell culture dish in the presence of differentiation media (DMEM/F12:Neurobasal 1:1, N2, B27 (Invitrogen), 2 mmol/l L-Glutamine, 1× MEM non-essential amino acids, 0.5% penicillin-streptomycin, 100 µmol/l β-2 mercaptoethanol and 20 ng/ml FGF-2). RA was added (Sigma-Aldrich, concentration 0.5 µmol/l) into fresh differentiation media on days 6, 10, and 14 after the beginning of EB development. On day 16, cells were dissociated using Accutase (Sigma-Aldrich) and plated on a gelatin-coated cell culture dish in maintenance media (DMEM/F12, N2, B27, L-Glutamine, MEM non-essential amino acids, 0.5% penicillin-streptomycin, 100 µmol/l β-2 mercaptoethanol, and 20 ng/ml FGF-2).

extract_protocol: as described in PMID: 19769940

value: Ctrl

tag: cell type

value: human embryonic stem cell derived NPCs


title: NPCs_from_CCTL14_p242_Ctrl

treatment_protocol: To induce neural differentiation, we utilized a protocol based on embryoid body (EB) formation with simultaneous all-trans-retinoic acid (RA) treatment. Colonies of hESCs were transferred to a non-adherent cell culture dish in the presence of differentiation media (DMEM/F12:Neurobasal 1:1, N2, B27 (Invitrogen), 2 mmol/l L-Glutamine, 1× MEM non-essential amino acids, 0.5% penicillin-streptomycin, 100 µmol/l β-2 mercaptoethanol and 20 ng/ml FGF-2). RA was added (Sigma-Aldrich, concentration 0.5 µmol/l) into fresh differentiation media on days 6, 10, and 14 after the beginning of EB development. On day 16, cells were dissociated using Accutase (Sigma-Aldrich) and plated on a gelatin-coated cell culture dish in maintenance media (DMEM/F12, N2, B27, L-Glutamine, MEM non-essential amino acids, 0.5% penicillin-streptomycin, 100 µmol/l β-2 mercaptoethanol, and 20 ng/ml FGF-2).

tag: treatment


title: YoungAdult_LyoVec_only_24hrs YA_8

description:
Sample ID: E382
Sample name: 6898350005_B
YoungAdult_LyoVec_only_24hrs

source_name: PBMC, young adult, LyoVec_only, 24h

tag: time


title: YoungAdult_No_treatment_24hrs YA_8

description:
Sample ID: E376
Sample name: 6898481080_K
YoungAdult_No_treatment_24hrs

source_name: PBMC, young adult, NoTx, 24h


title: hESCs_CCTL14_p242_Ctrl

growth_protocol: as described in PMID: 20960514

treatment_protocol: Ctrl cells

value: human embryonic stem cell

tag: cell line


title: YoungAdult_No_treatment_6hrs YA_8

description:
Sample ID: E373
Sample name: 6898368101_D
YoungAdult_No_treatment_6hrs

source_name: PBMC, young adult, NoTx, 6h

value: peripheral blood mononuclear cells (PBMCs)


title: 9247377118_R03C02

description: technical replicate: 9247377118_R05C02

value: sensitized


title: YoungAdult_Poly_IC_24hrs YA_8

description:
Sample ID: E370
Sample name: 7018861051_F
YoungAdult_Poly_IC_24hrs

source_name: PBMC, young adult, PolyIC, 24h


title: 9247377118_R02C02


title: hESCs_CCTL14_p22_16hrs_UVC

treatment_protocol: cells treated with UVC light and harvested 16hrs later

value: 16hrs UVC


title: hESCs_CCTL14_p22_8hrs_UVC

treatment_protocol: cells treated with UVC light and harvested 8hrs later

value: 8hrs UVC


title: 9247377111_R06C02


title: 9247377118_R03C01

description: technical replicate: 9247377118_R05C01


title: 9247377111_R05C02

value: MALE


title: 9247377118_R01C01


title: 9247377111_R03C02


title: 9247377118_R01C02

value: nonallergic


title: YoungAdult_Rig_I_24hrs YA_8

description:
Sample ID: E365
Sample name: 7018861099_C
YoungAdult_Rig_I_24hrs

source_name: PBMC, young adult, Rig I, 24h

value: Rig I


title: 9247377118_R04C01

description: technical replicate: 9247377118_R06C01


title: hESCs_CCTL14_p22_Ctrl


title: 9247377111_R04C02


title: 9247377111_R05C01


title: 9247377111_R04C01


title: hESCs_CCTL14_p22_4hrs_UVC

treatment_protocol: cells treated with UVC light and harvested 4hrs later

value: 4hrs UVC


title: YoungAdult_CLO_97_24hrs YA_8

description:
Sample ID: E346
Sample name: 7018879026_A
YoungAdult_CLO_97_24hrs

source_name: PBMC, young adult, CLO_97, 24h


title: 9247377111_R02C02


title: INS1E Noninfected_Cell_control_72_hour

city: Shatin, New Territories

first: Wai Yip

last: Lam

address: Area 39, Lo Kwee-Seong Integrated Biomedical Sciences Building

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: miRNA expression in pancreatic islet cells after 72 hours of incubation.

hyb_protocol: Labeled RNA was purified and hybridized to Agilent miRNA arrays with eight identical arrays per slide, with each array containing probes interrogating 699 rat miRNAs.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent Technologies) using the standard settings for 8x15k array slides (miRBase v16).

data_processing: Fluorescence intensity was calculated using Feature Extraction software (Vsn. 10.5.1.1, Agilent) and analysis performed using Genespring GX (Agilent) and Excel (Microsoft, WA). GeneSpring defaults with the percentile shift to the 50th percentile; hence raw signal to 1.0, normalisation by percentile shift to the 50th percentile, and no baseline transformation.

organism: Rattus norvegicus

source_name: 72 hour cell control

label_protocol: MiRNAs were labeled using the Agilent miRNA labeling reagent and hybridized to Agilent human miRNA arrays according to the manufacturer's protocol. Briefly, total RNA (100 ng) was dephosphorylated and ligated with 3', 5'-cytidine bisphosphate (pCp-Cy3).

growth_protocol: The clonal rat β-cell line INS-1E, derived from parental INS-1 cells was cultured as monolayers in RPMI-1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/mL streptomycin (all from Gibco, Life Technology, Rockville, Md., USA) at 37°C in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from normal and infected INS-1E cells using Trizol reagent (Invitrogen) following the manufacturer's protocol at time points 48, 72 hours post-infection. RNA pellets were resuspended in RNase-free water. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: INS-1E cells were grown to confluence in sterile T75 tissue culture flasks for the inoculation of virus isolate at a multiplicity of infection (m.o.i.) of one. After 1 hour of absorption, the virus was removed and 2 ml of fresh RPMI-1640 media with 2% FBS, 100 U/ml penicillin, 100 μg/mL streptomycin (all from Gibco, Life Technology) was added, and incubated at 37oC in 5% CO2 humidified air.

value: pancreatic islet cells


title: 9247377118_R02C01


title: INS1E COXB4_infected_48_hour

description: miRNA expression in pancreatic islet cells after 48 hours of Coxsackie B4 virus infection.

source_name: 48 hour COXB4 infected cells


title: 9247377111_R01C01


title: 9247377111_R02C01


title: YoungAdult_LPS_6hrs YA_8

description:
Sample ID: E355
Sample name: 7018861099_F
YoungAdult_LPS_6hrs

source_name: PBMC, young adult, LPS, 6h

value: LPS


title: 9247377111_R01C02


title: YoungAdult_CLO_97_6hrs YA_8

description:
Sample ID: E343
Sample name: 7018879019_F
YoungAdult_CLO_97_6hrs

source_name: PBMC, young adult, CLO_97, 6h


title: YoungAdult_LyoVec_only_24hrs YA_7

description:
Sample ID: E334
Sample name: 6898350005_D
YoungAdult_LyoVec_only_24hrs


title: 9020331172_R06C02


title: YoungAdult_LyoVec_only_6hrs YA_7

description:
Sample ID: E331
Sample name: 6990990031_I
YoungAdult_LyoVec_only_6hrs


title: INS1E Noninfected_Cell_control_48_hour

description: miRNA expression in pancreatic islet cells after 48 hours of incubation.

source_name: 48 hour cell control


title: 9247377111_R03C01


title: YoungAdult_Poly_IC_6hrs YA_8

description:
Sample ID: E367
Sample name: 7018861084_K
YoungAdult_Poly_IC_6hrs

source_name: PBMC, young adult, PolyIC, 6h

value: PolyIC


title: RIN5F COXB4_infected_72_hour

description: miRNA expression in pancreatic islet cells after 72 hours of Coxsackie B4 infection.

source_name: 72 hour COXB4 infected cells

growth_protocol: The RIN-5F cell line (ATCC® CRL-2058, Rockville, MD, USA) was a clone derived from the RIN rat islet cells which is an insulin-secreting rat cell line - was cultured as monolayers in RPMI-1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/mL streptomycin (all from Gibco, Life Technology, Rockville, Md., USA) at 37°C in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from normal and infected RIN-5F cells using Trizol reagent (Invitrogen) following the manufacturer's protocol at time points 48, 72 hours post-infection. RNA pellets were resuspended in RNase-free water. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: RIN-5F cells were grown to confluence in sterile T75 tissue culture flasks for the inoculation of virus isolate at a multiplicity of infection (m.o.i.) of one. After 1 hour of absorption, the virus was removed and 2 ml of fresh RPMI-1640 media with 2% FBS, 100 U/ml penicillin, 100 μg/mL streptomycin (all from Gibco, Life Technology) was added, and incubated at 37oC in 5% CO2 humidified air.