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Human and mouse genome assemblies customized for rDNA mapping

epigenetics genome-annotation genome-assembly genome-visualization rdna repetitive-dna ribosome transcription

rdna-mapping-genomes's Introduction

Human and Mouse genome assemblies customized for rDNA mapping, with annotation files and sample tracks

Files accompanying 'Construction and validation of customized genomes for human and mouse ribosomal DNA mapping.' George SS, Pimkin M, Paralkar VR. JBC (2023) are deposited here.

This repository contains publicly accessible customized versions of Human hg19 (GRCh37), hg38 (GRCh38), hs1 (T2T-CHM13) and Mouse mm10 (GRCm38), mm39 (GRCm39) genomes optimized for rDNA mapping with an additional chromosome R (chrR). Also contains annotation BED files depicting rDNA promoters, rRNA transcribed region, and intergenic spacer (IGS) regions on chrR, along with positive and negative control tracks (BWs) used for overall pipeline validation in the above preprint.

The contents of the gzipped tarball files are as follows:

  1. Human

    i.a. Human_hg19-rDNA_genome_v1.0.tar.gz (871 MB): Contains hg19 (GRCh37) genome masked for rDNA-like regions, with reference NCBI Genbank KY962518.1 rDNA sequence modified (as described in preprint) and inserted as an additional chrR.

    • hg19-rDNA_v1.0.fa and hg19-rDNA_v1.0.fa.fai

    i.b. Human_hg19-rDNA_genome_v1.0_annotation.tar.gz (3.10 MB): Contains standard RefSeq gene annotations for hg19 (GRCh37) with additional custom annotations for chrR. Also contains a Snapgene file with nucleotide sequence and annotation details for modified reference NCBI Genbank KY962518.1 rDNA sequence.

    • hg19-rDNA_v1.0.bed
    • Human_KY962518.1_Modified_Snapgene.dna

    i.c. Human_hg19-rDNA_genome_v1.0_control_tracks.tar.gz (1.98 GB): Contains hg19 (GRCh37) BigWigs (.bw) generated by applying the workflow described in the above preprint to positive (CTCF; TBP; POLR1A; UBTF), negative (EP300), and background (matching Input or IgG) controls.

    • CTCF_Human_hg19-rDNA.bw and InputForCTCF_Human_hg19-rDNA.bw
    • TBP_Human_hg19-rDNA.bw and IGGForTBP_Human_hg19-rDNA.bw
    • POLR1A_Human_hg19-rDNA.bw and InputForPOLR1A_Human_hg19-rDNA.bw
    • UBTF_Human_hg19-rDNA.bw and InputForUBTF_Human_hg19-rDNA.bw
    • EP300_Human_hg19-rDNA.bw and IGGForEP300_Human_hg19-rDNA.bw

    ii.a. Human_hg38-rDNA_genome_v1.0.tar.gz (984 MB): Contains hg38 (GRCh38) genome masked for rDNA-like regions, with reference NCBI Genbank KY962518.1 rDNA sequence modified (as described in preprint) and inserted as an additional chrR.

    • hg38-rDNA_v1.0.fa and hg38-rDNA_v1.0.fa.fai

    ii.b. Human_hg38-rDNA_genome_v1.0_annotation.tar.gz (3.10 MB): Contains standard RefSeq gene annotations for hg38 (GRCh38) with additional custom annotations for chrR. Also contains a Snapgene file with nucleotide sequence and annotation details for modified reference NCBI Genbank KY962518.1 rDNA sequence.

    • hg38-rDNA_v1.0.bed
    • Human_KY962518.1_Modified_Snapgene.dna

    ii.c. Human_hg38-rDNA_genome_v1.0_control_tracks.tar.gz (2.05 GB): Contains hg38 (GRCh38) BigWigs (.bw) generated by applying the workflow described in the above preprint to positive (CTCF; TBP; POLR1A; UBTF), negative (EP300), and background (matching Input or IgG) controls.

    • CTCF_Human_hg38-rDNA.bw and InputForCTCF_Human_hg38-rDNA.bw
    • TBP_Human_hg38-rDNA.bw and IGGForTBP_Human_hg38-rDNA.bw
    • POLR1A_Human_hg38-rDNA.bw and InputForPOLR1A_Human_hg38-rDNA.bw
    • UBTF_Human_hg38-rDNA.bw and InputForUBTF_Human_hg38-rDNA.bw
    • EP300_Human_hg38-rDNA.bw and IGGForEP300_Human_hg38-rDNA.bw

    iii.a. Human_hs1-rDNA_genome_v1.0.tar.gz (972 MB): Contains hs1 (T2T-CHM13) genome masked for rDNA-like regions, with reference NCBI Genbank KY962518.1 rDNA sequence modified (as described in preprint) and inserted as an additional chrR.

    • hs1-rDNA_v1.0.fa and hs1-rDNA_v1.0.fa.fai

    iii.b. Human_hs1-rDNA_genome_v1.0_annotation.tar.gz (2.90 MB): Contains standard RefSeq gene annotations for hs1 (T2T-CHM13) with additional custom annotations for chrR. Also contains a Snapgene file with nucleotide sequence and annotation details for modified reference NCBI Genbank KY962518.1 rDNA sequence.

    • hs1-rDNA_v1.0.bed
    • Human_KY962518.1_Modified_Snapgene.dna

    iii.c. Human_hs1-rDNA_genome_v1.0_control_tracks.tar.gz (2.10 GB): Contains hs1 (T2T-CHM13) BigWigs (.bw) generated by applying the workflow described in the above preprint to positive (CTCF; TBP; POLR1A; UBTF), negative (EP300), and background (matching Input or IgG) controls.

    • CTCF_Human_hs1-rDNA.bw and InputForCTCF_Human_hs1-rDNA.bw
    • TBP_Human_hs1-rDNA.bw and IGGForTBP_Human_hs1-rDNA.bw
    • POLR1A_Human_hs1-rDNA.bw and InputForPOLR1A_Human_hs1-rDNA.bw
    • UBTF_Human_hs1-rDNA.bw and InputForUBTF_Human_hs1-rDNA.bw
    • EP300_Human_hs1-rDNA.bw and IGGForEP300_Human_hs1-rDNA.bw

  2. Mouse

    i.a. Mouse_mm10-rDNA_genome_v1.0.tar.gz (870 MB): Contains mm10 (GRCm38) genome masked for rDNA-like regions, with reference NCBI Genbank BK000964.3 rDNA sequence modified (as described in preprint) and inserted as an additional chrR.

    • mm10-rDNA_v1.0.fa and mm10-rDNA_v1.0.fa.fai

    i.b. Mouse_mm10-rDNA_annotation_v1.0.tar.gz (2.30 MB): Contains standard RefSeq gene annotations for mm10 (GRCm38) with additional custom annotations for chrR. Also contains a Snapgene file with nucleotide sequence and annotation details for modified reference NCBI Genbank BK000964.3 rDNA sequence.

    • mm10-rDNA_v1.0.bed
    • Mouse_BK000964.3_Modified_Snapgene.dna

    i.c. Mouse_mm10-rDNA_control_tracks_v1.0.tar.gz (2.07 GB): Contains mm10 (GRCm38) BigWigs (.bw) generated by applying the workflow described in the above preprint to positive (CTCF; TBP; POLR1A; UBTF), negative (EP300), and background (matching Input or IgG) controls.

    • CTCF_Mouse_mm10-rDNA.bw and InputForCTCF_Mouse_mm10-rDNA.bw
    • TBP_Mouse_mm10-rDNA.bw and IGGForTBP_Mouse_mm10-rDNA.bw
    • POLR1A_Mouse_mm10-rDNA.bw and InputForPOLR1A_Mouse_mm10-rDNA.bw
    • UBTF_Mouse_mm10-rDNA.bw and IGGForUBTF_Mouse_mm10-rDNA.bw
    • EP300_Mouse_mm10-rDNA.bw and IGGForEP300_Mouse_mm10-rDNA.bw

    ii.a. Mouse_mm39-rDNA_genome_v1.0.tar.gz (871 MB): Contains mm39 (GRCm39) genome masked for rDNA-like regions, with reference NCBI Genbank BK000964.3 rDNA sequence modified (as described in preprint) and inserted as an additional chrR.

    • mm39-rDNA_v1.0.fa and mm39-rDNA_v1.0.fa.fai

    ii.b. Mouse_mm39-rDNA_annotation_v1.0.tar.gz (2.20 MB): Contains standard RefSeq gene annotations for mm39 (GRCm39) with additional custom annotations for chrR. Also contains a Snapgene file with nucleotide sequence and annotation details for modified reference NCBI Genbank BK000964.3 rDNA sequence.

    • mm39-rDNA_v1.0.bed
    • Mouse_BK000964.3_Modified_Snapgene.dna

    ii.c. Mouse_mm39-rDNA_control_tracks_v1.0.tar.gz (2.07 GB): Contains mm39 (GRCm39) BigWigs (.bw) generated by applying the workflow described in the above preprint to positive (CTCF; TBP; POLR1A; UBTF), negative (EP300), and background (matching Input or IgG) controls.

    • CTCF_Mouse_mm39-rDNA.bw and InputForCTCF_Mouse_mm39-rDNA.bw
    • TBP_Mouse_mm39-rDNA.bw and IGGForTBP_Mouse_mm39-rDNA.bw
    • POLR1A_Mouse_mm39-rDNA.bw and InputForPOLR1A_Mouse_mm39-rDNA.bw
    • UBTF_Mouse_mm39-rDNA.bw and IGGForUBTF_Mouse_mm39-rDNA.bw
    • EP300_Mouse_mm39-rDNA.bw and IGGForEP300_Mouse_mm39-rDNA.bw

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rdna-mapping-genomes's Issues

Using chrR ref genome with STAR

Hi,
Thank you for putting these reference genomes together! They've been very helpful for my work.

I'd like to use hg38-rDNA_v1.0.fa to map an RNAseq dataset using STAR. How should the annotation file, hg38-rDNA_v1.0.bed, be adapted for compatibility with STAR's .gtf format?

Best

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