The manually prepared K-562 single cells were pooled and sequenced using 2x75 bp sequencing on an Illumina NextSeq 500 (Illumina Inc., San Diego, CA, USA). Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq v1.9.0. Bulk and STORM-seq K562 libraries were pooled and 2x50 bp sequencing was performed on an Illumina NovaSeq 6000 sequencer using a 100 bp S2 sequencing kit (Illumina Inc., San Diego, CA, USA). Patient 1 fallopian tube epithelium STORM-seq libraries were also sequenced on a NovaSeq 6000 sequencer using a 2x100 bp S2 sequencing kit. Patient 2 fallopian tube epithelium STORM-seq libraries were sequenced on a Hiseq 4000 using a 2x150 bp sequencing kit at Fulgent Genetics. Base calling was done by Illumina NovaSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq v1.9.0. Base calling for the HiSeq sequencing run was performed at Fulgent Genetics and returned as FASTQ files.
Bcl2fastq v1
Manufactured by Illumina
Sourced in United States
Bcl2fastq v1.8.4 is a software tool developed by Illumina to convert base call (BCL) files generated by Illumina sequencing instruments into standard FASTQ format files. This tool is designed to facilitate downstream bioinformatics analysis of sequencing data.
Automatically generated - may contain errors
Lab products found in correlation
Agilent dna high sensitivity chip, by Agilent Technologies (22 mentions)
Quantifluor dsdna system, by Promega (19 mentions)
Novaseq 6000 sequencer, by Illumina (14 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (10 mentions)
Real time analysis v1, by Illumina (10 mentions)
Nextseq control software v2, by Illumina (10 mentions)
Hiseq 2500, by Illumina (8 mentions)
Qubit dsdna hs assay kit, by Thermo Fisher Scientific (7 mentions)
Nextseq 500 sequencer, by Illumina (7 mentions)
Nanodrop 2000, by Thermo Fisher Scientific (6 mentions)
Truseq ud indexed adapters, by Illumina (5 mentions)
Kapa mrna hyperprep kit v4.17, by Roche (5 mentions)
Truseq nano dna library preparation kit, by Illumina (4 mentions)
Truseq stranded mrna library preparation kit, by Illumina (4 mentions)
Nextseq 500, by Illumina (4 mentions)
Bioo scientific nextflex adapters, by PSC Biotech (4 mentions)
Kapa rna hyperprep kit, by Roche (4 mentions)
Qiaseq fastselect rrna hmr kit, by Qiagen (4 mentions)
Kapa hyper prep kit, by Roche (4 mentions)
Qubit fluorometer, by Thermo Fisher Scientific (3 mentions)
78 protocols using bcl2fastq v1
1
Single-cell RNA-seq of K562 and Fallopian Tube Epithelium
2
Metagenomic DNA Extraction and Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA was extracted from 600 μL of BAL sample using the NucleoSpin Soil kit (Macherey-Nagel, Düren, Germany) as described previously [17 (link)] except that bead beating was performed for 20 min. DNA was eluted twice with 2 × 30 μL of elution buffer SE of the NucleoSpin Soil kit. Purified DNA was stored at −20 °C. DNA concentration was measured using the Qubit fluorometer with Qubit dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, USA) as recommended by the manufacturer. Paired-end metagenomic DNA libraries were prepared from 100 ng DNA using the Ovation Rapid Multiplex DR System 1–96 (Nugen, San Carlos, CA, USA) and size-selected at about 300–400 bp (including adapters). The libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) using the 2 × 100 base paired end method at LGC Genomics (Berlin, Germany). Demultiplexed fastq files were generated from base-calls using Illumina’s bcl2fastq v1.8.4 software (Illumina, San Diego, CA, USA). Clipping of sequencing adapter remnants was performed using proprietary LGC Genomics software (LGC, Teddington, Middlesex, UK).
3
ChIP-seq for Histone H3K27Ac in Brain Tissue
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
ChIP was performed essentially as described in detail in our previous study [37 (link)]. Briefly, brain tissue dissected from 3 animals was pooled, homogenized, and fixed in PBS with 1% formaldehyde for 10 minutes. Nuclei were prepared from the fixed cells and stored at -80°C until use. Thawed nuclei were sonicated using a BiorupterTM UCD-200 (Diagenode, Liège, Belgium) sonicator, and fragmented chromatin was processed for ChIP with 2 ug histone H3K27Ac antibody per sample (Abcam ab4729), using one million nuclei for each IP. IPs were performed in biological replicate, with one pool of 3 samples in each replicate, as previously described. Libraries were prepared from eluted DNA using KAPA LTP library kits (KK8230) using Bioo Scientific index adapters, size-selected using AmpureXP beads (Beckman Coulter, Brea, CA, USA) and quality checked by Qubit 2.0 and Bioanalyzer (Agilent 2100). Samples were sequenced to a depth of 20-30M reads per replicate on an Illumina HiSeq 2500 sequencer using a TruSeq SBS sequencing kit, version 4, in single-end format with fragment length of 100 bp. Base calling and demultiplexing into FASTQ files was done using bcl2fastq v1.8.4 software (Illumina, San Diego, CA, USA).
4
High-Depth Targeted Sequencing Protocol
5
Illumina Sequencing Data Preprocessing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
All samples were de-multiplexed using Illumina’s bcl2fastq (v1.84) software with default settings for adapter trimming (at least 90% of bases should match) and allowing no mismatch per sequencing bar code (–mismatches 0). Raw Illumina reads were cleared from potential adapter contamination, quality controlled, and, if necessary, trimmed in paired-end mode using BBDuk from the BBMap package version 34.41 (https://sourceforge.net/projects/bbmap/ ). To pass the quality filter, read quality needed to surpass a Phred score of 20 and achieve a minimal length of 50 bp after trimming of low quality and adapter bases.
Additional data quality control measures were taken: each sample was tested before and after trimming with the FastQC to evaluate per base sequence quality, average base composition, GC content, sequence length distribution and adapter contaminations (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).
Additional data quality control measures were taken: each sample was tested before and after trimming with the FastQC to evaluate per base sequence quality, average base composition, GC content, sequence length distribution and adapter contaminations (
6
RNA-seq Analysis of Zebrafish Embryonic Stages
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA from 3 to 5 embryos at the indicated stages were prepared using the RNA Clean & Concentrator Kit (R1019, Zymo Research). cDNA library was constructed with the TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) and sequenced with the NextSeq 500/550 High Output Kit V2 (FC-404-2005, Illumina). Illumina bcl2fastq (v1.8.4) software was used for base calling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The number of raw reads mapped to genes was calculated by RSEM (rsem-1.2.4), the reference genome using danRer10, then put all the sample results together and normalized by EDAseq (1.99.1), gene expression fold change was calculated using normalized raw reads. The downstream analysis was performed using glbase scripts. Reads were deposited with GEO under the accession number GSE102032.
7
Genomic DNA Extraction and Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genomic DNA was isolated from the 16 evolved clones and the ancestor NRC-1 using an Epicentre MasterPure Gram Positive DNA Extraction Kit and a modified procedure. Lysozyme was omitted, and DNA purity and concentration was determined using a Thermo Scientific NanoDrop 2000. Genomic DNA was sequenced at the Michigan State University Research Technology Support Facility (RTSF) Genomics Core. Libraries were prepared using the Illumina TruSeq Nano DNA library preparation kit for Illumina MiSeq sequencing and loaded on a MiSeq flow cell after library validation and quantitation. Sequencing was completed using a 2- by 250-bp paired-end format using Illumina 500 cycle V2 reagent cartridge. Illumina Real Time Analysis (RTA) v1.18.54 performed base calling, and the output of the RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.8.4.
8
Illumina HiSeq 2500 Sequencing Data Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Initial image analysis and base calling were performed using RTA v1.18.61 (HCS v2.2.58; Illumina, San Diego, CA) on an Illumina HiSeq 2500. Bcl2fastq v1.8.4 (Illumina, San Diego, CA) was used to demultiplex the data into individual samples based on the indexes used during the library preparation. Since over 90 % of the reads had sequence quality scores over Q33 and the lowest mean quality score per sample (per base) was 27, reads were not trimmed based on quality and the raw sequence data was used for further analysis. As per manufacturer’s recommendations, the first three bases were trimmed from reads derived from the SMART method.
9
Soil Microbiome Profiling via Illumina Sequencing
10
Illumina MiSeq Sequencing Data Preprocessing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
BCL2FASTQ v.1.8.4 (Illumina, San Diego, CA, USA) was used to convert the base calls into forward, index1, index2 and reverse FASTQ files. In order to obtain more accurate and reliable results in subsequent bioinformatics analysis, the raw data was pre-processed using an in-house procedure as following: 1) Sequence reads not having an average quality of 20 over a 30 bps sliding window based on the phred algorithm were truncated, and trimmed reads having less than 75% of their original length, as well as their paired reads, were removed; 2) Removal of reads contaminated by adapters; 3) Removal of reads with ambiguous bases (N bases), and their paired reads; 4) Removal of reads with low complexity. Paired-end reads were generated using the Illumina MiSeq platform, and the reads with sequencing adapters, N bases, poly-bases, and low quality bases were filtered out using default parameters. If two paired-end reads overlapped with 1) a minimum overlap of 15 bp and 2) a mismatching ratio in the overlapped region <= 0.1, the consensus sequence was generated by FLASH v1.2.11 (Magoč and Salzberg 2011 (link)). Paired-end reads without overlaps were removed.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!