192 genes TaqMan Low Density Array – MIQE checklist
Sample Description
Rutin Liquid-Based Cytology (LBC) Cervical Samples arrived in PreservCyt. Shipped at room temperature, stored at 4-8 °C until use.
Volume/mass of sample processed
RNA isolation was carried out from 1 ml LBC sample.
RNA extraction
We used the RecoverAllTM Total nucleic Acid Isolation Kit (Ambion; Cat# AM1975) according to protocol of the manufacturer. DNase-treatment was carried out on column (ingredient of the kit) for 30 minutes at room temperature according to protocol of the manufacturer. Volume of extracted RNA samples were 60 µl. Extracted RNA samples were stored at -80 °C. DNA contamination was not checked. Nucleic acid quantification was not performed.
Reverse Transcription
We used the TaqMan Reverse Transcription Reagents Kit (Applied Biosystems; Cat# N808-0234).
Storage of cDNA
cDNA samples were stored at -20 °C.
List of genes examined
Gene_Symbol / Gene_Name / HS ID (Applied Biosystems)ALOX12B / arachidonate 12-lipoxygenase, 12R type / Hs00153961_m1
ISL1 / ISL1 transcription factor, LIM/homeodomain, (islet-1) / Hs00158126_m1
S100A7 / S100 calcium binding protein A7 (psoriasin 1) / Hs00161488_m1
TGM1 / transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase) / Hs00165929_m1
KRT10 / "keratin 10 (epidermolytic hyperkeratosis; keratosis palmaris et plantaris)" / Hs00166289_m1
ALOX12 / arachidonate 12-lipoxygenase / Hs00167524_m1
CYP24A1 / cytochrome P450, family 24, subfamily A, polypeptide 1 / Hs00167999_m1
TNFSF9 / tumor necrosis factor (ligand) superfamily, member 9 / Hs00169409_m1
DSG1 / desmoglein 1 / Hs00170047_m1
RHCG / Rhesus blood group, C glycoprotein / Hs00170975_m1
CXCL9 / chemokine (C-X-C motif) ligand 9 / Hs00171065_m1
GREM1 / gremlin 1 homolog, cysteine knot superfamily (Xenopus laevis) / Hs00171951_m1
ACPP / acid phosphatase, prostate / Hs00173475_m1
HAT (TMPRSS11D) / airway trypsin-like protease / Hs00173695_m1
IL1A / interleukin 1, alpha / Hs00174092_m1
CAMK4 / calcium/calmodulin-dependent protein kinase IV / Hs00174318_m1
AIM2 / absent in melanoma 2 / Hs00175457_m1
LAMP3 / lysosomal-associated membrane protein 3 / Hs00180880_m1
FGFBP1 / fibroblast growth factor binding protein 1 / Hs00183226_m1
DKK1 / dickkopf homolog 1 (Xenopus laevis) / Hs00183740_m1
SERPINB5 / serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5 / Hs00985285_m1
CEACAM7 / carcinoembryonic antigen-related cell adhesion molecule 7 / Hs00185152_m1
SCEL / sciellin / Hs00187213_m1
KYNU / kynureninase (L-kynurenine hydrolase) / Hs00187560_m1
CHI3L2 / chitinase 3-like 2 / Hs00187790_m1
ARSF / arylsulfatase F / Hs00187832_m1
SULT2B1 / sulfotransferase family, cytosolic, 2B, member 1 / Hs00190268_m1
NEF3 (NEFM) / neurofilament 3 (150kDa medium) / Hs00193572_m1
BENE (MALL) / BENE protein / Hs00193728_m1
S100P / S100 calcium binding protein P / Hs00195584_m1
KRT1 / keratin 1 (epidermolytic hyperkeratosis) / Hs00196158_m1
SPINK5 / serine protease inhibitor, Kazal type 5 / Hs00199260_m1
SERPINB3 / serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3 / Hs00199468_m1
CLCA4 / chloride channel, calcium activated, family member 4 / Hs00201697_m1
IL1F5 / interleukin 1 family, member 5 (delta) / Hs00202179_m1
SERPINB13 / serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13 / Hs00202640_m1
DUOX2 / dual oxidase 2 / Hs00204187_m1
C4.4A / GPI-anchored metastasis-associated protein homolog / Hs00205233_m1
TFCP2L2 (GRHL1) / transcription factor CP2-like 2 / Hs00205742_m1
C1orf10 / chromosome 1 open reading frame 10 / Hs00211833_m1
TMPRSS4 / transmembrane protease, serine 4 / Hs00212669_m1
DEFB103A / defensin, beta 103A / Hs00218678_m1
PRV1 (CD177) / polycythemia rubra vera 1 / Hs00360669_m1
DSG3 / desmoglein 3 (pemphigus vulgaris antigen) / Hs00170075_m1
NICE-1 (CRCT1) / NICE-1 protein / Hs00219416_m1
IL1F9 / interleukin 1 family, member 9 / Hs00219742_m1
CLDN1 / claudin 1 / Hs00221623_m1
ALOXE3 / arachidonate lipoxygenase 3 / Hs00222134_m1
GPR87 / G protein-coupled receptor 87 / Hs00225057_m1
SARG (C1orf116) / specifically androgen-regulated protein / Hs00225127_m1
FLJ22671 (C2orf54) / hypothetical protein FLJ22671 / Hs00227510_m1
CDKN2A / cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) / Hs00233365_m1
STAT3 / signal transducer and activator of transcription 3 (acute-phase response factor) / Hs00234174_m1
CXCL6 / chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) / Hs00237017_m1
CEACAM5 / carcinoembryonic antigen-related cell adhesion molecule 5 / Hs00237075_m1
SLCO4A1 / solute carrier organic anion transporter family, member 4A1 / Hs00249583_m1
AKR1B10 / aldo-keto reductase family 1, member B10 (aldose reductase) / Hs00252524_m1
DIO2 / deiodinase, iodothyronine, type II / Hs00255341_m1
NEBL / nebulette / Hs00255521_m1
ECG2 (SPINK7) / esophagus cancer-related gene-2 / Hs00261445_m1
RNASE7 / ribonuclease, RNase A family, 7 / Hs00261482_m1
C20orf114 / chromosome 20 open reading frame 114 / Hs00264197_m1
SCGB2A2 / secretoglobin, family 2A, member 2 / Hs00267190_m1
PITX1 / paired-like homeodomain transcription factor 1 / Hs00267528_m1
CCL18 / chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated) / Hs00268113_m1
GJB2 / gap junction protein, beta 2, 26kDa (connexin 26) / Hs00269615_s1
CEBPD / CCAAT/enhancer binding protein (C/EBP), delta / Hs00270931_s1
SPRR3 / small proline-rich protein 3 / Hs00271304_m1
GJB6 / gap junction protein, beta 6 (connexin 30) / Hs00272726_s1
IL1RN / interleukin 1 receptor antagonist / Hs00277299_m1
RDH12 / retinol dehydrogenase 12 (all-trans and 9-cis) / Hs00288401_m1
ABCA12 / ATP-binding cassette, sub-family A (ABC1), member 12 / Hs00292421_m1
RDH-E2 / retinal short chain dehydrogenase reductase / Hs00331485_m1
CALML3 / calmodulin-like 3 / Hs00359114_s1
DEFA5 / defensin, alpha 5, Paneth cell-specific / Hs00360716_m1
KRT5 / keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types) / Hs00361185_m1
CDKN2B / cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) / Hs00365249_m1
LILRB1 / leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1 / Hs00366806_m1
CLECSF7 / C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7 / Hs00369958_m1
FAM3D / family with sequence similarity 3, member D / Hs00371132_m1
PITX2 / paired-like homeodomain transcription factor 2 / Hs00374154_m1
WFDC5 / WAP four-disulfide core domain 5 / Hs00377339_m1
APOBEC3A / apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A / Hs00377444_m1
MGC21394 (SPINK6) / protease inhibitor H / Hs00381837_m1
GJB5 / gap junction protein, beta 5 (connexin 31.1) / Hs00383058_m1
FSTL5 / follistatin-like 5 / Hs00393783_m1
SERPINB9 / serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 9 / Hs00394497_m1
DEFB4 / defensin, beta 4 / Hs00823638_m1
UNQ467 (KRTDAP) / KIPV467 / Hs00415563_m1
LILRA1 / leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1 / Hs00429037_m1
CLDN4 / claudin 4 / Hs00533616_s1
FOXE1 / forkhead box E1 (thyroid transcription factor 2) / Hs00916085_s1
FLJ25680 (POU5F2) / hypothetical protein FLJ25680 / Hs00541903_s1
K5B (KRT78) / keratin 5b / Hs00542779_m1
C18orf26 / chromosome 18 open reading frame 26 / Hs00543432_m1
CLDN7 / claudin 7 / Hs00600772_m1
IL19 / interleukin 19 / Hs00604657_m1
KRTHA4 (KRT34) / keratin, hair, acidic, 4 / Hs00606019_gH
STMN2 / stathmin-like 2 / Hs00606370_m1
ULBP2 / UL16 binding protein 2 / Hs00607609_mH
ADH7 / alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide / Hs00609447_m1
LASS3 / LAG1 longevity assurance homolog 3 (S. cerevisiae) / Hs00698859_m1
SERPINB4 / serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4 / Hs00741313_g1
C9orf140 / chromosome 9 open reading frame 140 / Hs00746788_s1
KRT6B / keratin 6B / Hs00749101_s1
KRT6E (KRT6C) / keratin 6E / Hs00752476_s1
SPRL6A (LCE3D) / small proline rich-like (epidermal differentiation complex) 6A / Hs00754375_s1
CXCL13 / chemokine (C-X-C motif) ligand 13 (B-cell chemoattractant) / Hs00757930_m1
MGC4766 (TEX101) / testis-specific protein TES101RP / Hs00758335_m1
CALML5 / calmodulin-like 5 / Hs00758617_s1
DCNP1 (C5orf20) / dendritic cell nuclear protein 1 / Hs00758645_s1
BPAG1 (DST) / bullous pemphigoid antigen 1, 230/240kDa / Hs00794953_m1
MT1H / metallothionein 1H / Hs00823168_g1
SPRR1B / small proline-rich protein 1B (cornifin) / Hs00824893_m1
IVL / involucrin / Hs00846307_s1
LILRA3 / leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3 / Hs00846590_s1
MMP12 / matrix metalloproteinase 12 (macrophage elastase) / Hs00899668_m1
EREG / epiregulin / Hs00914313_m1
SLC6A14 / solute carrier family 6 (neurotransmitter transporter), member 14 / Hs00200601_m1
ADAMDEC1 / ADAM-like, decysin 1 / Hs00205545_m1
KRT24 / keratin 24 / Hs00219278_m1
TP73L (TP63) / tumor protein p73-like / Hs00978338_m1
CLCA2 / chloride channel, calcium activated, family member 2 / Hs00197957_m1
KLK8 / kallikrein 8 (neuropsin/ovasin) / Hs01012737_m1
DESC1 (TMPRSS11E) / DESC1 protein / Hs01070171_m1
KLK13 / kallikrein 13 / Hs00210264_m1
KLK5 / kallikrein 5 / Hs01548153_m1
SERPINB8 / serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8 / Hs00160071_m1
DKFZp686G0786 (DGB6) / hypothetical protein DKFZp686G0786 / Hs01584201_m1
CYP2C18 / cytochrome P450, family 2, subfamily C, polypeptide 18 / Hs01595322_mH
STAT3 / signal transducer and activator of transcription 3 (acute-phase response factor) / Hs00234174_m1
ENOX2 / ecto-NOX disulfide-thiol exchanger 2 / Hs00197268_m1
SPRR2C / small proline-rich protein 2C / Hs00272438_m1
TMPRSS11A / transmembrane protease, serine 11A / Hs00856105_mH
ACADVL / acyl-Coenzyme A dehydrogenase, very long chain / Hs00817723_g1
LGALS7 / lectin, galactoside-binding, soluble, 7 (galectin 7) / Hs00170104_m1
PKP1 / plakophilin 1 (ectodermal dysplasia/skin fragility syndrome) / Hs00913276_m1
ICHYN / ichthyin protein / Hs00398027_m1
JCS1 / "Unknown" / Hs00290676_s1
JCS2 / "Unknown" / Hs00419349_m1
LUZP2 / leucine zipper protein 2 / Hs00300694_s1
MAD; RY1 (MXD1) / "MAX dimerization protein 1;putative nucleic acid binding protein RY-1" / Hs00231137_m1
JCS3 / "Unknown" / Hs00329958_s1
MU7C5AC / mucin 5AC, oligomeric mucus/gel-forming / Hs01365601_m1
EFCAB5 / EF-hand calcium binding domain 5 / Hs00417644_m1
FUT6 / fucosyltransferase 6 (alpha (1,3) fucosyltransferase) / Hs00173404_m1
PRUNE2 / prune homolog 2 (Drosophila) / Hs00322421_m1
ZNF543 / zinc finger protein 543 / Hs00411200_m1
PERF15 / lipid-binding protein / Hs00908573_m1
SEC14L3 / SEC14-like 3 (S. cerevisiae) / Hs00545462_m1
KIAA1086 / KIAA1086 / Hs00392866_m1
ATP6V0A4 / ATPase, H+ transporting, lysosomal V0 subunit a isoform 4 / Hs00220986_m1
ANGPT4 / angiopoietin 4 / Hs00211115_m1
PLEKHK1 / pleckstrin homology domain containing, family K member 1 / Hs00377175_m1
"SSX4;SSX6" / "synovial sarcoma, X breakpoint 4;synovial sarcoma, X breakpoint 6" / Hs00601718_m1
TRIM16 / tripartite motif-containing 16 / Hs00232396_m1
MGC13102 (TMEM79) / hypothetical protein MGC13102 / Hs00260483_m1
MBL2 / mannose-binding lectin (protein C) 2, soluble (opsonic defect) / Hs00175093_m1
CEACAM8 / carcinoembryonic antigen-related cell adhesion molecule 8 / Hs00266198_m1
TFAP2A / transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha) / Hs01029413_m1
ALMS1 / Alstrom syndrome 1 / Hs00367316_m1
CAPN5 / calpain 5 / Hs00182791_m1
TLR8 / toll-like receptor 8 / Hs00152972_m1
JCS4 / "Unknown" / Hs00418678_m1
3'HEXO (THEX1) / 3' exoribonuclease / Hs00297850_m1
MTTP / microsomal triglyceride transfer protein (large polypeptide, 88kDa) / Hs00165177_m1
DKFZP434N1235 (SLC25A31) / hypothetical protein DKFZp434N1235 / Hs00229864_m1
JCS5 / "Unknown" / Hs00418007_m1
KIRREL3 / kin of IRRE like 3 (Drosophila) / Hs00287375_m1
BATF / basic leucine zipper transcription factor, ATF-like / Hs00232390_m1
RAI3 (GPRC5A) / retinoic acid induced 3 / Hs00173681_m1
JCS6 / "Unknown" / Hs00417340_m1
DMRT2 / doublesex and mab-3 related transcription factor 2 / Hs00246364_m1
BTLA / B and T lymphocyte associated / Hs00699198_m1
C20orf179 / chromosome 20 open reading frame 179 / Hs00708912_s1
PSMB8 / proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional peptidase 7) / Hs00544758_m1
ANK1 / ankyrin 1 / Hs00220867_m1
DCP2 / decapping enzyme hDcp2 / Hs00400333_m1
SERPINB7 / serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7 / Hs01562791_m1
NUMBL / numb homolog (Drosophila)-like / Hs00191080_m1
KCNB2 / potassium voltage-gated channel, Shab-related subfamily, member 2 / Hs00191116_m1
FLJ10116 (MREG) / hypothetical protein FLJ10116 / Hs00215942_m1
IL26 / interleukin 26 / Hs00218189_m1
IL2RA / interleukin 2 receptor, alpha / Hs00166229_m1
PIK3AP1 / phosphoinositide-3-kinase adaptor protein 1 / Hs00381030_m1
TRIM14 / tripartite motif-containing 14 / Hs00207648_m1
RERE / arginine-glutamic acid dipeptide (RE) repeats / Hs00201558_m1
SH2D2A / SH2 domain protein 2A / Hs00610216_m1
CYP7B1 / cytochrome P450, family 7, subfamily B, polypeptide 1 / Hs00191385_m1
IL21R / interleukin 21 receptor / Hs00222310_m1
CYP19A1 / cytochrome P450, family 19, subfamily A, polypeptide 1 / Hs00240671_m1
· "_m" in HS ID indicates an assay whose probe spans an exon junction and will not detect genomic DNA
· "_s" indicates an assay whose primers and probes are designed within a single exon, such assays will, by definition detect genomic DNA
· "_g" indicates an assay that may detect genomic DNA. The assay primers and probe may also be within a single exon.
· "_mH," "_sH", or "_gH" indicates that the assay was designed to a transcript belonging to a gene family with high sequence homology. The assays have been designed to give between 10 Ct and 15Ct difference between the target gene and the gene with the closest sequence homology. This means that an assay will detect the target transcript with 1,000-30,000-fold greater discrimination (sensitivity) than the closest homologous transcript, if they are present at the same copy number in a sample.
Platform used
Applied Biosystems 7900HT Fast Real-Time PCR System
Applied Biosystems TaqMan Low Density Array Format 96a (Number of targets and controls: 95+1; Number of assay replicates: 2; Number of samples per card: 2; Catalog number: 4342259)
Polymerase/Buffer/Kit identity and Manufacturer