KOLF2.1Jv1.1 Assembly

The personalized diploid genome of the KOLF iPSC cell line. KOLF2.1J is the parental iPSC line and serves as a reference cell line for distributed iPSC derivatives. It has a relatively stable karyotype, maintains pluripotency, exhibits consistent growth characteristics, and harbors fewer problematic structural abnormalities compared to other iPSC lines. Therefore, generating a complete telomere-to-telomere (T2T) diploid assembly for this valuable resource is warranted, as it would enable broad community use and facilitate the characterization of its personalized variants and genomic features.

For more data analysis and assembly procedures, please see the original paper:

• Alvarez Jerez, P., Rhie, A., Kim, J., Hebbar, P., Nag, S., Antipov, D., ... & Blauwendraat, C. (2026). The complete genome of the KOLF2. 1J reference iPSC line. bioRxiv, 2026-03.

Latest assembly releases

v1.1 (2026)

• KOLF2.1Jv1.1.noY.fa : T2T reconstruction of 45 chromosomes of KOLF iPSC line, except chrY and, include chrM, you can download this from here.

SUBID	BioProject	BioSample	Accession	Organism
SUB16212997	PRJNA1471455	SAMN60427383	JBZDRB000000000	Homo sapiens iPSC (primary)
SUB16212997	PRJNA1471454	SAMN60427383	JBZDRC000000000	Homo sapiens iPSC (alternate)

• This genome is viewable in the T2T UCSC browser.

Downloads

Liftover resources

• 1:1 Liftover T2T-CHM13v2.0 <-> KOLF2.1Jv1.1, see here.
  • KOLF2.1Jv1.1 primary <-> T2T-CHM13v2.0 :
    • KOLF2.1Jv1.1.pri_vs_chm13v2.chain
    • KOLF2.1Jv1.1.pri_vs_chm13v2.inverted.chain
  • KOLF2.1Jv1.1 alternative <-> T2T-CHM13v2.0 :
    • KOLF2.1Jv1.1.alt_vs_chm13v2.chain
    • KOLF2.1Jv1.1.alt_vs_chm13v2.inverted.chain
• 1:1 Liftover KOLF2.1Jv1.1 primary <-> alternative, see here.
  • KOLF2.1Jv1.1 primary <-> KOLF2.1Jv1.1 alternative :
    • KOLF2.1Jv1.1.pri_vs_alt.chain
    • KOLF2.1Jv1.1.pri_vs_alt.inverted.chain

WGS Alignments

• All alignments on the diploid assembly, excluding chrY, have been stored here.
• Illumina
  • KOLF_IPS.noY.bam
• ONT
  • KOLF_ASTRO_IND12.sorted.noY.bam
  • KOLF_ASTRO_NYSCF.sorted.noY.bam
  • KOLF_IPS.mapped.sorted.noY.bam
  • KOLF_IPSC_UL.noY.bam
  • KOLF_MGL.mapped.sorted.noY.bam
  • KOLF_NEURON.mapped.sorted.noY.bam
  • KOLF_NGN2.mapped.sorted.noY.bam
• PacBio
  • KOLF_IPSC_PACBIO.noY.bam

Methylation profile

• Methylation calls from ONT data are provided in BED file format by cell type and can be downloaded here.
  • ASTRO_IND12.mrg.modkit.pri.bed.gz
  • ASTRO_NYSCF.mrg.modkit.pri.bed.gz
  • IPS.mrg.modkit.pri.bed.gz
  • MGL.mrg.modkit.pri.bed.gz
  • NEURON.mrg.modkit.pri.bed.gz
  • NGN2.mrg.modkit.pri.bed.gz

HiC alignment

• HiC aligned on the primary haplotype, you can download this from here.
  • iMicroglia.kolf2.1Jv1.1pri.autosomes_X_M.bam
  • iPSc.kolf2.1Jv1.1pri.autosomes_X_M.bam

Gene annotation

• Gene annotations for both haplotypes are available for download here.
  • KOLF_MAT.gff3
  • KOLF_PAT_noY.gff3
• The list of genes including novel genes is available using Google Cloud Bucket
  • gs://asap-raw-team-indipd-ipsc-lr-wgs-kolf21j-wt/annotations/KOLF_genes_with_novel_isoforms.csv

Transcriptome sequencing data alignments

All transcriptomic sequencing data are available for download here.

• ONT direct sequencing data
  • ASTRO_IND12.ONT.noY.bam
  • ASTRO_NYSCF.ONT.noY.bam
  • IPS.ONT.noY.bam
  • MGL.ONT.noY.bam
  • NEURON.ONT.noY.bam
  • NGN2.ONT.noY.bam
  • OLIGO_NYSCF.ONT.noY.bam
• PacBio ISOSEQ sequencing data
  • MGL_WT_1.noY.bam
  • MGL_WT_2.noY.bam
  • MGL_WT_3.noY.bam
• Illumina bulk RNA sequencing data
  • ipsc_illumina_hg38.noY.bam

Variant calls

SV calls and heterozygosity sites are also available for download here.

• SV calling
  • hapdiff_phased.sv.noY.bed
• The heterozygosity site between primary and alternative haplotype
  • hetsites.hetsites.fix.bed.gz

CAGE sequencing alignments

• CAGE sequencing data from the KOLF2.1J reference line for iPSC, cortical neuron, and microglia. This data was generated by DNAform. Average length from all three cell types is 75bp at around 3Gb per cell. Please visit here.
  • KOLF.IPS.noY.bam
  • KOLF.Neuron.noY.bam
  • KOLF.iMGL.noY.bam

Contact

Please raise issues on this Github repository concerning this dataset.

Citation

Alvarez Jerez, P., Rhie, A., Kim, J., Hebbar, P., Nag, S., Antipov, D., ... & Blauwendraat, C. (2026). The complete genome of the KOLF2. 1J reference iPSC line. bioRxiv, 2026-03.

History

Feb  25,  2026  v1.1 assembly released.
Apr  7,   2026  Additional alignment data listed.
Jun  10,  2026  T2T UCSC browser for primary and alternative haplotypes are available.