The above-described sequential-ChIP samples, including input DNA, ChIP control samples (ChIP without antibodies), and sequential-ChIP samples (pulled down with α-Atf1 and α-Flag antibodies), were used for next-generation sequence analysis. We prepared a library from the eluted DNA samples using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (NEB, MA) with the END repair/dA-tailing module and Index primers (NEB, MA). Sequencing was conducted by Eurofins Genomics (Eurofins Scientific, Luxembourg). Read-mapping was carried out as previously described (29 (link)). The sequential-ChIP seq data are available at DDBJ Sequence Read Archive (DRA) (https://www.ddbj.nig.ac.jp/dra/index.html , accession number: DRA011814).
Index primers
Manufactured by New England Biolabs
Index primers are short oligonucleotide sequences used in next-generation sequencing library preparation to uniquely identify samples. They enable the pooling of multiple samples for sequencing, allowing for efficient and cost-effective use of sequencing capacity.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using index primers
1
Sequential ChIP-seq Library Preparation
2
Yeast DNA Enrichment and Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) with index primers (NEB, E7335, E7710 and E7600). Fragmented genomic DNA from S. cerevisiae (Cell Signaling, 40366) was used (10 pg per sample) as spike-in.
DNA libraries were sequenced (150 bp × 2) with NovaSeq 6000 (Illumina), and the initial 50 bases of each read were aligned to a concatenation of human reference genome (GRCh38) and S. cerevisiae (sacCer3) with a BWA algorithm bwa mem (version 0.7.17) (Li and Durbin 2009 (link)). Duplications of reads were marked with a Picard tool MarkDuplicates (version 2.18.9) (http://broadinstitute.github.io/picard ). Only a minority of the aligned reads constituted the yeast genome, thereby confirming the successful recovery of DNA fragments cleaved by pAG-MNase. A subset of aligned reads was selected for the downstream analyses using Samtools (version 1.9) with the following commands: SAM flag 3 (read paired; read mapped in proper pair) (samtools view -f 3); mapping quality greater than 20 (samtools view -q 20); without tags “XA:Z:” and “SA:Z:” (grep -v -e ‘XA:Z:’ -e ‘SA:Z:’); and aligned in either one of the chromosomes chr1 to chr22, chrX or chrY (samtools view chr1 chr2 ... chrY).
DNA libraries were sequenced (150 bp × 2) with NovaSeq 6000 (Illumina), and the initial 50 bases of each read were aligned to a concatenation of human reference genome (GRCh38) and S. cerevisiae (sacCer3) with a BWA algorithm bwa mem (version 0.7.17) (Li and Durbin 2009 (link)). Duplications of reads were marked with a Picard tool MarkDuplicates (version 2.18.9) (
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!