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Hiseq 2500 rapid run

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The HiSeq 2500 Rapid Run is a high-throughput DNA sequencing system manufactured by Illumina. It is designed to generate large volumes of sequencing data quickly and efficiently. The system uses Illumina's proprietary sequencing-by-synthesis technology to perform DNA sequencing. The HiSeq 2500 Rapid Run is capable of sequencing multiple samples simultaneously, allowing for rapid generation of sequencing data.

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Lab products found in correlation

Truseq adapter, by Illumina (4 mentions) Flow cell, by Illumina (2 mentions) Ampure bead, by Beckman Coulter (2 mentions) Kapa high throughput library preparation kit, by Roche (2 mentions) Qubit dsdna hs kit, by Thermo Fisher Scientific (2 mentions) Standard pcr library amplification, by Roche (2 mentions) 2100 bioanalyzer, by Agilent Technologies (2 mentions) Ampure xp bead, by Beckman Coulter (2 mentions) Paired end v1 kit, by Illumina (2 mentions) Qiamp dna micro kit, by Qiagen (1 mentions) Truseq technology, by Illumina (1 mentions) High dna sensitivity bioanalyzer 2500, by Agilent Technologies (1 mentions) Library quantification kit, by Illumina (1 mentions) Turbo dnase, by Thermo Fisher Scientific (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Rna pico kit, by Agilent Technologies (1 mentions) Truseq stranded total rna sample prep guide, by Illumina (1 mentions) Bioanalyzer high sensitivity dna kit, by Agilent Technologies (1 mentions) Qubit fluorometer, by Qiagen (1 mentions)

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HiSeq 2500 (12028 citations) HiSeq run (12 citations) HiSeq 2500 Rapid (10 citations) HiSeq 2500 Rapid Run flow cell (10 citations) HiSeq 2500 Rapid Run platform (9 citations) HiSeq Rapid Run (7 citations) HiSeq 2500 Rapid Run Flow Cell (v1) (3 citations) HiSeq 2500 Rapid Run flow cell (v2) (2 citations) HiSEQ 2500 Rapid Run sequencer (2 citations)

17 protocols using hiseq 2500 rapid run

1

Comprehensive RASL Sequencing Workflow

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A total of three biological replicates were processed independently. Each biological replicate consisted of 384-well plates (four male and four female, for a total of eight plates), with a sample size of 3,072. The 9,216 samples from the three replicates were pooled together and data was obtained in a single sequencing run, therefore eliminating a major source of batch effects. The RASL pool was sequenced using two lanes of an Illumina HiSeq 2500 Rapid Run.
Simon J.M., Paranjape S.R., Wolter J.M., Salazar G, & Zylka M.J. (2019). High-throughput screening and classification of chemicals and their effects on neuronal gene expression using RASL-seq. Scientific Reports, 9, 4529.
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2

Integrated Single-Cell Sequencing of Transcripts and Antibodies

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Drop-seq was performed as described1 (link) with modifications. For the human/mouse mixing experiment cells were loaded at a concentration of 400 cells/µL to achieve a high doublet rate. For PMBC experiments cells were loaded at 150 cells/µL. cDNA was amplified for 10 cycles and products were then size separated with Ampure Beads (Beckman Coulter, USA) into <300 nt fragments containing antibody derived tags (ADTs) and >300 nt fragments containing cDNAs derived from cellular mRNA. ADTs were amplified 10 additional cycles using specific primers that append P5 and P7 sequences for clustering on Illumina flowcells. Alternatively, antibody tags can be amplified directly from thoroughly washed Drop-seq beads after RNA-cDNA amplification using specific primers for the antibody oligo and Drop-seq bead-RT oligo. cDNAs derived from mRNA were converted into sequencing libraries by tagmentation as described1 (link). After quantification, libraries were merged at appropriate concentrations (10% of a lane for ADT, 90% cDNA library). Sequencing was performed on a HiSeq 2500 Rapid Run with v2 chemistry per manufacturer’s instructions (Illumina, USA). See supplementary protocol for a more detailed description.
Stoeckius M., Hafemeister C., Stephenson W., Houck-Loomis B., Chattopadhyay P.K., Swerdlow H., Satija R, & Smibert P. (2017). Large-scale simultaneous measurement of epitopes and transcriptomes in single cells. Nature methods, 14(9), 865-868.
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3

Integrated Single-Cell Sequencing of Transcripts and Antibodies

Cited 1 time
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Drop-seq was performed as described1 (link) with modifications. For the human/mouse mixing experiment cells were loaded at a concentration of 400 cells/µL to achieve a high doublet rate. For PMBC experiments cells were loaded at 150 cells/µL. cDNA was amplified for 10 cycles and products were then size separated with Ampure Beads (Beckman Coulter, USA) into <300 nt fragments containing antibody derived tags (ADTs) and >300 nt fragments containing cDNAs derived from cellular mRNA. ADTs were amplified 10 additional cycles using specific primers that append P5 and P7 sequences for clustering on Illumina flowcells. Alternatively, antibody tags can be amplified directly from thoroughly washed Drop-seq beads after RNA-cDNA amplification using specific primers for the antibody oligo and Drop-seq bead-RT oligo. cDNAs derived from mRNA were converted into sequencing libraries by tagmentation as described1 (link). After quantification, libraries were merged at appropriate concentrations (10% of a lane for ADT, 90% cDNA library). Sequencing was performed on a HiSeq 2500 Rapid Run with v2 chemistry per manufacturer’s instructions (Illumina, USA). See supplementary protocol for a more detailed description.
Stoeckius M., Hafemeister C., Stephenson W., Houck-Loomis B., Chattopadhyay P.K., Swerdlow H., Satija R, & Smibert P. (2017). Large-scale simultaneous measurement of epitopes and transcriptomes in single cells. Nature methods, 14(9), 865-868.
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4

Chromium Single Cell 3' RNA-Seq Protocol

Cited 2 times
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Samples were processed using the Chromium Single Cell 3′ Solution v2 chemistry (10 × Genomics, CA, USA) as per the manufacturer’s recommendations24 (link). Briefly, cell suspension is resuspendeed at 1 × 106 cells per ml. To generate GEMs, master mix with cell suspension, gel beads and partioning oils are loaded on Chromium Chip. GEM-RT reaction, cDNA amplification, gene expression library generation were followed using Chromium kits and reagents. After library generation, sequencing was performed using Illumina HiSeq 2500 Rapid run with 98-bp pair-end reads. Using Cell Ranger (version 2.0, 10 × Genomics), the fastq files were generated from the bcl files. The sequence reads were aligned to UCSC hg38 and UMIs (Unique Molecular Identifiers) were counted for each gene in each cell barcode using Cell Ranger count (option: –expect_cells = 6000). Then, the data were polished by R package Seurat as below26 (link),27 (link).
Kashima Y., Togashi Y., Fukuoka S., Kamada T., Irie T., Suzuki A., Nakamura Y., Shitara K., Minamide T., Yoshida T., Taoka N., Kawase T., Wada T., Inaki K., Chihara M., Ebisuno Y., Tsukamoto S., Fujii R., Ohashi A., Suzuki Y., Tsuchihara K., Nishikawa H, & Doi T. (2021). Potentiality of multiple modalities for single-cell analyses to evaluate the tumor microenvironment in clinical specimens. Scientific Reports, 11, 341.
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5

Single-cell RNA-seq of Wild-type and FACS Samples

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The capturing of single cells was performed on the Chromium Single-cell 3′ v2. For the two wild-type samples, a target of 3000 cells per run was set; however, the capture rate was below this in both samples. For the FACS samples the whole suspension was loaded for capturing. The following cDNA synthesis with PCR and library preparation were done according to the manufacturers guidelines. Sequencing was done using Illumina HiSeq 2500 Rapid Run. The Cell Ranger pipeline (version 2.0.0 or 2.1.1) together with the mouse transcriptome mm10 were used to align the reads and to generate the gene-cell matrices.
Kupari J., Häring M., Agirre E., Castelo-Branco G, & Ernfors P. (2019). An Atlas of Vagal Sensory Neurons and Their Molecular Specialization. Cell Reports, 27(8), 2508-2523.e4.
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6

Whole Metagenome and VLP Sequencing

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DNA sequencing was performed using Illumina HiSeq 2500 Rapid Run at 150 cycles in paired-end mode. DNA concentration and quality was determined using the Qubit dsDNA HS kit (Invitrogen) and a Bioanalyzer 2100 (Agilent, Santa Clara, CA). DNA libraries were prepared using a KAPA High Throughput Library Preparation Kit with standard PCR library amplification (KAPA Biosystems, Wilmington, MA). TruSeq adapters (Illumina, San Diego, CA) with 6 bp indices were used to enable multiplexed sequencing. Illumina libraries were size selected using AMPure XP beads (Beckman Coulter, Indianapolis, IN). Library quality was measured on a Bioanalyzer 2100 by product size and concentration. On average, 43 million paired-end whole metagenome reads and 30 million paired-end VLP reads were generated for each sample. Sequencing reads were demultiplexed using the 6 bp TruSeq adapter sequences allowing for one mismatch using the Illumina CASAVA software. DNA quality control, HiSeq 2500 sequencing and library preparation was performed by the UT Southwestern Eugene McDermott Center for Human Growth and Development Next Generation Sequencing Core.
Duerkop B.A., Kleiner M., Paez-Espino D., Zhu W., Bushnell B., Hassell B., Winter S.E., Kyrpides N.C, & Hooper L.V. (2018). Murine colitis reveals a disease-associated bacteriophage community. Nature microbiology, 3(9), 1023-1031.
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7

Microbiome Profiling of Intestinal Samples

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Dissected intestines were placed in 2-mL screw cap tubes with 0.1 mm zirconia silica beads and 200-μL sterile lysis buffer (20 mM Tris-Cl; 2 mM EDTA; 2.5-mL 20% Tx-100) and frozen in liquid nitrogen. DNA was extracted using Qiamp DNA micro Kit (Qiagen) as detailed in S1 Text. The microbial communities of each sample were characterized by an Illumina HiSeq 2500 Rapid Run (San Diego, CA) sequencing the 16S rRNA gene amplicon by the University of Oregon Genomics and Cell Characterization Facility. The read length was paired-end 150 nucleotide, targeting the V4 region (primers listed in S2 Table). The 16S rRNA gene Illumina reads were clustered using USEARCH 8.1.1803 [64 (link)]. The final OTU table was rarefied to a depth of 100,000 (see S2 Data for metadata, S3 Data for OTU taxonomy, and S4 Data for OTU table). Measures of community diversity and similarity (OTU richness, phylogenetic distances, unweighted UniFrac) were calculated in R using vegan, picante, and GUniFrac (See S2 Code). Correlations were calculated in R, and false discovery rate was adjusted using the Benjamini & Hochberg correction in p.adjust (See S1 Code).
Rolig A.S., Mittge E.K., Ganz J., Troll J.V., Melancon E., Wiles T.J., Alligood K., Stephens W.Z., Eisen J.S, & Guillemin K. (2017). The enteric nervous system promotes intestinal health by constraining microbiota composition. PLoS Biology, 15(2), e2000689.
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8

Metatranscriptomics Library Preparation

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Libraries for metatranscriptomics analysis were prepared from total RNA using a protocol modified from Stewart et al., (2010) (link). Briefly, rRNA was depleted using probes synthesized by PCR from DNA collected at each sampling depth (Supplementary Methods). Messenger RNA was amplified from rRNA-depleted total RNA using random hexamer primers, then double-stranded cDNA was prepared using reverse transcriptase and second strand synthesis kits. Libraries (~225 bp insert) were prepared using Illumina TruSeq technology. Samples were pooled and run on one lane of 150 × 2 Illumina HiSeq 2500 Rapid Run at HudsonAlpha Genomic Services. Reads have been deposited in the NCBI SRA under accession number SRP068308 (Bioproject PRJNA308451).
Edwardson C.F, & Hollibaugh J.T. (2017). Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA. The ISME Journal, 11(10), 2195-2208.
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9

RNA-seq of Gab1 ERVK RLTR15 Embryos

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RNA was extracted from E12.5 yolk sac, placenta, and whole embryo from F4E1 (Gab1 ERVK RLTR15 +/+), F4E3 (Gab1 ERVK RLTR15 +/+), F4E5 (Gab1 ERVK RLTR15 +/−), and F5E6 (Gab1 ERVK RLTR15 +/+) embryos using RNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions. RNA was treated with TURBO DNase (Thermo Fisher Scientific), and quality was assessed with RNA Pico Kit (Agilent) on the Agilent 2100 Bioanalyzer (RIN > 8.7 for all samples). mRNA sequencing libraries were generated using SmartSeq v4 cDNA generation and Nextera XT library preparation, as per manufacturers’ instructions. The quantification of all libraries was done using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification kit (KAPA). Libraries were sequenced using 125 bp paired-end on the Illumina HiSeq 2500 RapidRun, multiplexing 12 samples over 2 lanes.
Hanna C.W., Pérez-Palacios R., Gahurova L., Schubert M., Krueger F., Biggins L., Andrews S., Colomé-Tatché M., Bourc’his D., Dean W, & Kelsey G. (2019). Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues. Genome Biology, 20, 225.
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10

cfDNA Library Preparation and Amplicon Sequencing

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Forty microliters of the extracted cfDNA from each case was used as input into library preparation using the Natera Library Prep Kit. All purified libraries were QC-ed on the LabChip GX 5k DNA chip. Successful libraries had a single peak at ~250 bp. The amplified libraries were then analyzed by mPCR-NGS. Optimal mPCR conditions were as described. Each PCR assay pool was used to amplify the SNV targets from the 10 corresponding samples and 20 negative control samples (plasma libraries prepared from healthy subjects). Each amplicon pool was sequenced on one Illumina HiSeq 2500 Rapid Run with 50 cycles paired-end reads using the Illumina Paired End v1 kit with an average target DOR of ~40,000 per assay.
Abbosh C., Birkbak N.J., Wilson G.A., Jamal-Hanjani M., Constantin T., Salari R., Le Quesne J., Moore D.A., Veeriah S., Rosenthal R., Marafioti T., Kirkizlar E., Watkins T.B., McGranahan N., Ward S., Martinson L., Riley J., Fraioli F., Al Bakir M., Grönroos E., Zambrana F., Endozo R., Bi W.L., Fennessy F.M., Sponer N., Johnson D., Laycock J., Shafi S., Czyzewska-Khan J., Rowan A., Chambers T., Matthews N., Turajlic S., Hiley C., Lee S.M., Forster M.D., Ahmad T., Falzon M., Borg E., Lawrence D., Hayward M., Kolvekar S., Panagiotopoulos N., Janes S.M., Thakrar R., Ahmed A., Blackhall F., Summers Y., Hafez D., Naik A., Ganguly A., Kareht S., Shah R., Joseph L., Quinn A.M., Crosbie P., Naidu B., Middleton G., Langman G., Trotter S., Nicolson M., Remmen H., Kerr K., Chetty M., Gomersall L., Fennell D., Nakas A., Rathinam S., Anand G., Khan S., Russell P., Ezhil V., Ismail B., Irvin-sellers M., Prakash V., Lester J., Kornaszewska M., Attanoos R., Adams H., Davies H., Oukrif D., Akarca A.U., Hartley J.A., Lowe H.L., Lock S., Iles N., Bell H., Ngai Y., Elgar G., Szallasi Z., Schwarz R.F., Herrero J., Stewart A., Quezada S.A., Peggs K.S., Van Loo P., Dive C., Lin J., Rabinowitz M., Aerts H.J., Hackshaw A., Shaw J.A., Zimmermann B.G, & Swanton C. (2017). Phylogenetic ctDNA analysis depicts early stage lung cancer evolution. Nature, 545(7655), 446-451.
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