Publications
Single-Cell
Note: Acknowledges Admera Health “for their invaluable contributions”
Dissociated cells were resuspended in ice-cold PBS containing 0.02% BSA and loaded onto a Chromium Single cell 3′ chip (with an estimated recovery of 6,000 cells per channel) to generate gel beads in emulsion (GEMs). scRNA-seq libraires were prepared with the Chromium Single cell 3′ GEM, Library & Gel Bead Kit v3 (10x Genomics, PN: 1000075). Libraries from different samples were pooled and sequenced by Admera Health on a NovaSeq S4 (Illumina) using 150 × 2 chemistry. Demultiplexing, alignment, barcode and UMI counting and aggregation were performed using Cell Ranger (v3.0 with default settings). This provided us with a feature by count matrix.
Bead Kit v2(10x Genomics, PN:120237). Libraries from different samples were pooled and sequenced by Admera Health on a NovaSeq S4 (Illumina) using 150*2 chemistry.
snRNA-seq libraries were prepared with the Chromium Single cell 3′ GEM, Library & Gel Bead Kit v3 (10x Genomics). Libraries from different samples were pooled and sequenced by Admera Health on a NovaSeq S4 (Illumina).
In order to reach sufficient DNA quantity, the extract was subjected to whole-genome amplification (WGA) with the REPLI-g Single Cell Kit (Qiagen). The WGA product was processed through a Nextera XT library and sequenced on an Illumina HiSeq X machine by Admera Health (South Plainfield, NJ, USA), producing 37,100,964 pairs of 150 bp reads.
RNA-seq/smallRNA
Libraries were analyzed using Illumina next-generation sequencing, and relative quantification was provided by Admera Health. Read counts were subjected to paired differential expression analysis using the R package DESeq2.51
Courtney KD, Ma Y, Diaz de Leon A, Christie A, Xie Z, Woolford L, Singla N, Joyce A, Hill H, Madhuranthakam AJ, Yuan Q, Xi Y, Zhang Y, Chang J, Fatunde O, Arriaga Y, Frankel AE, Kalva S, Zhang S, McKenzie T, Reig Torras O, Figlin RA, Rini BI, McKay RM, Kapur P, Wang T, Pedrosa I, Brugarolas J. HIF-2 Complex Dissociation, Target Inhibition, and Acquired Resistance with PT2385, a First-in-Class HIF-2 Inhibitor, in Patients with Clear Cell Renal Cell Carcinoma. Clin Cancer Res. 2020 Feb 15;26(4):793-803. doi: 10.1158/1078-0432.CCR-19-1459. Epub 2019 Nov 14. PMID: 31727677; PMCID: PMC7024660.
High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer.
Echeverria GV, Powell E, Seth S, Ge Z, Carugo A, Bristow C, Peoples M, Robinson F, Qiu H, Shao J, Jeter-Jones SL, Zhang X, Ramamoorthy V, Cai S, Wu W, Draetta G, Moulder SL, Symmans WF, Chang JT, Heffernan TP, Piwnica-Worms H. High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer. Nat Commun. 2018 Nov 29;9(1):5079. doi: 10.1038/s41467-018-07406-4. PMID: 30498242; PMCID: PMC6265294.
Grozdanov PN, Masoumzadeh E, Kalscheuer VM, Bienvenu T, Billuart P, Delrue MA, Latham MP, MacDonald CC. A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans. Nucleic Acids Res. 2020 Sep 25;48(17):9804-9821. doi: 10.1093/nar/gkaa689. PMID: 32816001; PMCID: PMC7515730.
SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice.
Lee KS, Wong TY, Russ BP, Horspool AM, Miller OA, Rader NA, Givi JP, Winters MT, Wong ZYA, Cyphert HA, Denvir J, Stoilov P, Barbier M, Roan NR, Amin MS, Martinez I, Bevere JR, Damron FH. SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice. PLoS One. 2022 Aug 29;17(8):e0273430. doi: 10.1371/journal.pone.0273430. PMID: 36037222; PMCID: PMC9423646.
Lin YH, Zhang S, Zhu M, Lu T, Chen K, Wen Z, Wang S, Xiao G, Luo D, Jia Y, Li L, MacConmara M, Hoshida Y, Singal AG, Yopp A, Wang T, Zhu H. Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury. Gastroenterology. 2020 May;158(6):1698-1712.e14. doi: 10.1053/j.gastro.2020.01.026. Epub 2020 Jan 20. PMID: 31972235; PMCID: PMC8902703.
Maier TR, Masonbrink RE, Vijayapalani P, Gardner M, Howland AD, Mitchum MG, Baum TJ. Esophageal Gland RNA-Seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode Heterodera glycines. Mol Plant Microbe Interact. 2021 Sep;34(9):1084-1087. doi: 10.1094/MPMI-03-21-0051-A. Epub 2021 Sep 29. PMID: 33900122.
Myles IA, Castillo CR, Barbian KD, Kanakabandi K, Virtaneva K, Fitzmeyer E, Paneru M, Otaizo-Carrasquero F, Myers TG, Markowitz TE, Moore IN, Liu X, Ferrer M, Sakamachi Y, Garantziotis S, Swamydas M, Lionakis MS, Anderson ED, Earland NJ, Ganesan S, Sun AA, Bergerson JRE, Silverman RA, Petersen M, Martens CA, Datta SK. Therapeutic responses to Roseomonas mucosa in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair. Sci Transl Med. 2020 Sep 9;12(560):eaaz8631. doi: 10.1126/scitranslmed.aaz8631. PMID: 32908007; PMCID: PMC8571514.jm
Piórkowska K, Żukowski K, Ropka-Molik K, Tyra M. Variations in Fibrinogen-like 1 (FGL1) Gene Locus as a Genetic Marker Related to Fat Deposition Based on Pig Model and Liver RNA-Seq Data. Genes (Basel). 2022 Aug 9;13(8):1419. doi: 10.3390/genes13081419. PMID: 36011329; PMCID: PMC9407393.
Fluorescently labeled Gli1+ cells, sorted from spinal cord or cortex were sent to Admera Health LLC to perform RNAseq.
RNA sequencing on BT333 patient derived cell lines was performed by Admera Health.
RNA-sequencing and analysis was performed as previously described [37]. Total RNA was isolated using TRIzol reagent (Invitrogen Corp., Carlsbad, CA) from the osteoclasts that were cultured for 14 days in osteogenic differentiation medium following the manufacturer's protocol and was submitted to Admera Health (South Plainsfield, NJ) who assessed sample quality with the Agilent Bioanalyzer and prepared the library using the NEBnext Ultra RNA - Poly-A kit. Libraries were analyzed using Illumina next generation sequencing and relative quantification was provided by Admera Health.
RNA-Seq was performed at Admera Health Biopharma (South Plainfield, NJ, United States).
RNA sequencing was conducted by Admera Health (South Plainfield, NJ) on the Hi-seq 2x150 platform.
WGS/WES
Exome capture sequencing of extracted DNA was done by IDTxGen lockdown human panel (Admera Health, LLC South Plainfield, NJ).
Captured nucleotides were subjected to 150–base pair paired-end sequencing on an Illumina HiSeq platform (Admera Health, South Plainfield, NJ).
Exome sequencing was performed by Admera Health.
Whole-exome sequencing (WES) was performed by Admera Health.
For WES, tumor DNA samples from 16 formalin-fixed, paraffin-embedded (FFPE) tumors and germline DNA samples from four buffy coats were extracted and sequenced at Admera Health.
Whole-exome sequencing (WES) was performed with an Illumina HiSeq platform (Admera Health, New Jersey), aiming for a 90% coverage of the IDT Xgen library, human genome version 38 (hg38, December 2013)
Exome capture sequencing of extracted DNA was done by IDTxGen lockdown human panel (Admera Health, LLC South Plainfield, NJ).
Whole Genome Sequencing and Variant Filtering DNA collected from the affected calf, the dam, the sire, and three paternal half-siblings was sent to Admera Health (South Plainfield, NJ) for KAPA library prep and 150 bp paired-end sequencing on an Illumina NovaSeq to a targeted sequencing depth of 12X
Libraries were sequenced on an Illumina MiSeq 2 × 150 platform (San Diego, CA, USA) through the Admera Health Company (South Plainfield, NJ, USA).
Purified libraries from each mouse were pooled at equal ratios based on lung weight to ensure even sequencing depth per cell, purified once more with Sera-Mag Select beads to remove excess free primers, and sequenced on the Illumina HiSeq 2500 or NextSeq 550 platform (Admera Health Biopharma Services).
The authors thank the patients who contributed specimens to this study; the Northwestern Skin Disease Research Center (DNA/RNA Delivery Core), the Robert H. Lurie Comprehensive Cancer Center (Pathology Core), the Center for Cancer Genome Discovery, the Yale Center for Genome Analysis, and Admera Health for their sequencing support;
We thank Admera Health for performing next generation sequencing
We would like to thank... and Admera Health (Yun Zhao) for genomics
The sperm DNA samples were sent to Admera Health (South Plainfield, NJ, United States), a CLIA-certified laboratory, for WGBS analyses.
Oh H, Grinberg-Bleyer Y, Liao W, Maloney D, Wang P, Wu Z, Wang J, Bhatt DM, Heise N, Schmid RM, Hayden MS, Klein U, Rabadan R, Ghosh S. An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function. Immunity. 2017 Sep 19;47(3):450-465.e5. doi: 10.1016/j.immuni.2017.08.010. Epub 2017 Sep 7. PMID: 28889947; PMCID: PMC5679261. Library preparation and sequencing were performed by Admera Health. Library was constructed on immunoprecipitated DNA according to manufacturer’s recommendations (KAPA Hyper Prep Kit).
Library preparation and sequencing were performed by Columbia University’s JP Sulzberger Genome Center and Admera Health.
The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq2000 in paired read mode with the read length of 150 nucleotides at the Admera Health.
DNA fragments were purified from the immunoprecipitated samples, and the corresponding control samples (Input; digested chromatin not subjected to immunoprecipitation) were sequenced on the Illumina platform (Admera Health, NJ, USA) in paired-end, 150 bp mode
Next-generation sequencing (NGS) library preparation and sequencing of one genomic DNA sample, one Input, and one ChIP sample (the first biological replicate using anti-Cg-CenH3) were performed by Admera Health facility (USA) on the Illumina HiSeqX platform, using multiplexing of the samples in a single lane.
The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq X Five/Ten sequencing systems in paired-end 150bp reads at the Admera Health.
The libraries were sequenced on Illumina’s HiSeq4000 in paired read mode with the read length of 150 nucleotides at the Admera Health.
ChIP-seq/ATAC-seq/CUT&RUN
Metagenomics
The V3-V4 region of the 16 S rRNA gene was targeted to obtain the fragment libraries, which were amplified as described by the Illumina protocol and with primers of Klindworth et al. [19] on an Illumina MiSeq sequencer with 2 × 300 bp chemistry by a provider known as Admera Health (South Plainfield, NJ, USA).
Expanding Antarctic biogeography: microbial ecology of Antarctic island soils
sent to Admera Health Biopharma Services (USA) for Illumina Hiseq whole genome shotgun sequencing.
The WGA product was processed through a Nextera XT library and sequenced on an Illumina HiSeq X machine by Admera Health (South Plainfield, NJ, USA), producing 37,100,964 pairs of 150 bp reads
Libraries were pooled and submitted to Admera Health (South Plainfield, NJ, United States)
Therefore, the DNA material obtained from WGA was processed with a Nextera XT library and sequenced at Admera Health (South Plainfield, USA), using Illumina HiSeq X technology to generate 75,709,674 and 74,962,776 reads (paired-ends 2 × 150 bp) for IPSal+sm and IPSal+b populations, respectively.
The libraries were sequenced at Admera Health, LLC (NJ, USA) using an Illumina HiSeq X sequencer (150-bp paired-end reads). Bioinformatics analysis was conducted using KBase.
Metatranscriptomics Analysis of Ileum Microbial Communities in Necrotic Enteritis Chickens
The library preparation and sequencing process was conducted at Genohub (Admera Health Biopharma Services) using the Universal Prokaryotic RNA-Seq Library Preparation Kit (Tecan, California, USA) for the library preparation and Illumina HiSeq system for the sequencing of total RNA
Finally, faecal shotgun metagenomics libraries of 3 biological replicates of 24-month-old AL, DR, AL_DR16M and AL_DR20M, and negative controls, were sequenced at 250x2 pairedend sequencing on an Illumina HiSeq 2500 at Admera Health, USA.
The sequencing was done on an Illumina MiSeq v2 platform by Admera Health, with 2x250bp paired end reads and a sequencing depth at 24-30M reads.
Libraries for sequencing were prepared using the Nextera XT library Prep Kit (Illumina) and sequenced on an HiSeq X in an external facility (Admera Health LLC, NJ, USA) in paired end, with 150 bp read long.
Risk Factors for Antimicrobial Resistance in Turkey Farms: A Cross-Sectional Study in Three European Countries
The samples were sequenced on the NovaSeq 6000 platform (Illumina Inc, CA, USA) by Admera Health (South Plainfield, NJ, USA), using a 2 × 150-bp paired-end (PE) read approach, aiming for 35 M PE reads per sample.
The shotgun sequencing was carried out by a commercial sequencing service provider (Admera Health, South Plainfield, NJ, USA).
were sequenced on an Illumina HiSeq 4000 (2 × 150 cycles, paired end) at Admera Health, New Jersey (USA).
Library preparation and sequencing of the Illumina data were conducted through Genohub (Austin, TX) and Admera Health (South Plainfield, NJ).
DNA was shipped for sequencing to an external provider (Admera Health, NJ, USA)
The construction of the library was carried out commercially (ADMERA HEALTH LLC, USA).
The FloraPrep™ sample collection tubes and primers were from Suzhou Admera Health Medical Technology Co., Ltd.
Metagenomes were sequenced using Illumina Nextseq (150 bp, paired-end reads) (Admera Health, NJ, USA).
Analysis for total bacteria, fungi and protist was performed via multiplex amplicon sequencing in a HiSeq 2500 System® - Rapid Mode 2 × 250 bp paired-end (Illumina Inc., San Diego, USA) in Admera Health (Admera Health, New Jersey, US).
The remaining samples (i.e., 56 samples) associated with long-term storage (4, 8, and 12 months) of P1 and S1 were sequenced on an Illumina HiSeq 4000 (2 × 150 cycles, paired end) at Admera Health, New Jersey (USA).
Libraries were sequenced using Illumina MiSeq v3 technology (2 × 300 bp, paired-end) by Admera Health (San Francisco, CA, USA) with 30% PhiX DNA as spike-in.
The construction of the library was done commercially (ADMERA HEALTH LLC, USA).
Fecal DNA samples were sequenced using the Illumina NovaSeq apparatus by Admera Health (USA).
Degradation profile of nixtamalized maize pericarp by the action of the microbial consortium PM-06
The sequencing of the extracted mgDNA (8 h samples), was carried out at Admera Health Inc. (NJ, USA), using the Illumina NextSeq platform.
The pooled PCR products were sequenced at an Illumina HiSeq 2X250bp at Admera Health (New Jersey, USA)
Samples were shipped on icepacks to Admera Health (South Plainfield, NJ) for DNA extraction and 16S rRNA sequencing using the Floracheck™ (Admera Health) Mammalian assay to determine the V3 and V4 hypervariable regions.
Up to 15 ng of isolated genomic DNA was used to amplify via PCR with proprietary primers (Admera Health) covering hypervariable regions V3 and V4
For library preparation, 50 ng of isolated genomic DNA were used and amplified via PCR with proprietary primers (Admera Health, NJ, USA) covering hypervariable regions V3 and V4.
Potential role of rumen bacteria in modulating milk production and composition of admixed dairy cows
Library preparation and sequencing were performed at Admera Health Limited (USA).
MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters
The four clonal libraries were sent to Admera Health (Plainfield, NJ, USA) for PacBio library preparation and sequencing
Methylseq
One μg of total DNA of each sample was sent for WGBS to Admera Health Biopharma Services.
Sequencing was performed on an Illumina HiSeq 2500 at the NIDDK genomics core and on an Illumina HiSeq X Ten by Admera Health.
Libraries were barcoded and shipped for pooling and sequencing at Admera Health Biopharma Services, generating 150 bp paired-end reads on two lanes of a HiSeq-X sequencer.
gDNA concentration was quantified at 0.5-1.5 μg (Qubit® dsDNA BR Assay Kit on a Qubit® 2.0. Fluorometer) and sent for Whole Genome Bisulfite Sequencing (WGBS) at Admera Health (New Jersey, USA).
WGBS-seq was performed at Admera Health Biopharma Services.
Whole-genome bisulfite sequencing (WGBS-seq) was performed at Admera Health Biopharma Services.
Reduced representation bisulfite sequencing (RRBS) libraries were pooled in groups of six and sequenced in a 75 bp single-end read on the NextSeq 550 system (Illumina) (Admera Health, La Jolla, CA, USA).
Samples were sequenced at Admera Health using an Illumina HiSeq 2x150 at sequencing depth of 40 million reads
CRISPR/Other
RNA sequencing and initial data analysis were performed at Admera Health (South Plainfield, NJ).
Tang R, Shuldiner EG, Kelly M, Murray CW, Hebert JD, Andrejka L, Tsai MK, Hughes NW, Parker MI, Cai H, Li YC, Wahl GM, Dunbrack RL, Jackson PK, Petrov DA, Winslow MM. Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth. Nat Cell Biol. 2023 Jan;25(1):159-169. doi: 10.1038/s41556-022-01049-w. Epub 2023 Jan 12. PMID: 36635501; PMCID: PMC10521195.
The libraries were pooled based on lung weight to ensure even sequencing depth, cleaned up again using AMPure XP beads, and sequenced (read length 2x150bp) on the Illumina HiSeq 2500 or NextSeq 500 platform (Admera Health Biopharma Services).
Each library was sequenced to obtain 250M of pair-end 150nt (PE150) reads on the HiSeq 4000 platform, by Biopharma Services at Admera Health, NJ
Libraries were 50bp paired-end sequenced on a NovaSeq X plus by Admera Health (South Plainfield, NJ.
RNA-seq libraries were subjected to paired-end sequencing (150 bp), targeting 80 M total reads per sample (40 M in each direction), on an Illumina HiSeq platform (Admera Health, LLC, South Plainfield, NJ, USA).
The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq2000 in paired read mode with the read length of 150 nucleotides at the Admera Health.
The DNA sequencing was performed by Admera Health (New Jersey, USA). Te integrity of the genomic DNA was visualized using 1% agarose gel electrophoresis in 0.5×TBE buffer.
Myung Chang Lee, Hongchen Cai, Christopher W. Murray, Chuan Li, Yan Ting Shue, Laura Andrejka, Andy L. He, Alessandra M.E. Holzem, Alexandros P. Drainas, Julie H. Ko, Garry L. Coles, Christina Kong, Shirley Zhu, ChunFang Zhu, Jason Wang, Matt van de Rijn, Dmitri A. Petrov, Monte M. Winslow, Julien Sage, A multiplexed in vivo approach to identify driver genes in small cell lung cancer,Cell Reports,Volume 42, Issue 1,2023,111990,ISSN 2211-1247,https://doi.org/10.1016/j.celrep.2023.111990.
Purified libraries from each mouse were pooled at equal ratios based on lung weight to ensure even sequencing depth per cell, purified once more with Sera-Mag Select beads to remove excess free primers, and sequenced on the Illumina HiSeq 2500 or NextSeq 550 platform (Admera Health Biopharma Services).
Consequently, ten composite mDNA preparations (from 8 salt pan and 2 halites, respectively) underwent library construction and sequencing by Admera Health, LCC (NJ, USA). The PCR-free KAPA Hyper prep kit was used for library preparation and paired-end reads of 150 bp were sequenced in a single lane using the Illumina HiSeq X platform.
Library preparation and sequencing were performed by Admera Health (South Plainfield, NJ, USA). For the gut fly-isolated strain, as well as for milk- (n = 8) and lung-tissue-isolated (n = 1) strains, assembly was conducted by Admera Health using SPAdes (v. 3.14.0) with parameter “-k 127.”
DiVito Evans A, Fairbanks RA, Schmidt P, Levine MT. Histone methylation regulates reproductive diapause in Drosophila melanogaster. PLoS Genet. 2023 Sep 13;19(9):e1010906. doi: 10.1371/journal.pgen.1010906. PMID: 37703303; PMCID: PMC10499233.
We extracted DNA from pools of 50 individuals from each focal inbred line (PA and FL) and sequenced these pools at 100x coverage (Admera Health, South Plainfield, NJ). we prepared 18 samples (PA diapause, PA persistently reproductive, PA age-matched control, FL diapause, FL persistently reproductive, and FL age-matched control) and 18 libraries using NEBNext Ultra II (directional) with Poly-A selection, and sequenced libraries using Illumina 2x150 for a total of 30M reads per sample (Admera Health Biopharma Services, South Plainfield, NJ).
Libraries were sequenced and demultiplexed by Admera Health using the Illumina NovaSeq S4 2 × 150.
Author Manuscript: Department of Biopharma Services, Admera Health, Holmdel, NJ, USA
Pooled samples were subjected to NextSeq or MiSeq for paired-end reads of 75 cycles at Admera Health, LLC (New Jersey, USA)
RNA-Seq was performed at Admera Health Biopharma (South Plainfield, NJ, United States).
The purified cDNA library products were evaluated using the Agilent bioanalyzer and sequenced on NextSeq High Output 1×75 (Admera Health Biopharma Services).
Sequencing was performed on Illumina HiSeq X with 150-bp PE reads. Sequencing was performed by Admera Health (South Plainfield, NJ).
Library preparation with TruSeq RNA Library Prep Kit (Illumina) and mRNA NGS sequencing (40×106 paired end read) were performed by Admera Health (South Plainfield, NJ).
A Chromium library was prepared using standard instructions, shipped to Admera Health (Plainsfield, NJ, USA) and bidirectionally sequenced using 150-bp reads on a lane of HiSeq X Ten (Illumina, Inc., San Diego, CA, USA).
These libraries were sequenced on an Illumina NextSeq 500 in the 2 × 150-bp paired-ended configuration (Admera Health Biopharma Services)
Shaer Tamar E, Kishony R. Multistep diversification in spatiotemporal bacterial-phage coevolution. Nat Commun. 2022 Dec 28;13(1):7971. doi: 10.1038/s41467-022-35351-w. PMID: 36577749; PMCID: PMC9797572.
Sequencing libraries were prepared according to Baym et al.74. and sequenced with Illumina HiSeq X machine to produce 150 base pairedend reads (Admera Health).
Total cellular RNA was subjected to RNA sequencing by using the QuantSeq FWD kit. Library preparation and sequencing were carried out by Admera Health (South Plainfield, NJ, USA).
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