CRISPR Indel Calling Demo Data
Additional Analysis Figures
Publications
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).