DOI: 10.5061/dryad.dz08kps5d
title: Telomere dataset used for calculating bulk and chromosome specific telomere length

description: Short telomeres cause age-related disease and long telomeres predispose to
 cancer; however, the mechanisms regulating telomere length are unclear. To
 probe these mechanisms,  we developed a nanopore sequencing
 method, Telomere Profiling, that identified mean telomere length to
 similar a Southern and to the clinical FlowFISH assay.  We mapped
 telomere reads to specific chromosome ends and, strikingly, could identify
 chromosome end-specific lengths that differed by more than 6kb. 
 We measured chromosome end-specific telomere lengths for 147 individuals
 and found that specific chromosome ends were consistently shorter or
 longer. This rank order of specific chromosome end telomere lengths was
 also found in newborn cord blood, suggesting telomere length is determined
 at birth. The average telomere length at birth was ~8kb +/- 250 bp,
 shorter than previously estimated. Understanding the mechanisms regulating
 length will allow deeper insights into telomere biology that can lead to
 new approaches to disease.
description: Telomeres were isolated and measured using telomere profiling
 protocol with Oxford Nanopore's MinION instrument and basecalled
 using ONT's guppy basecaller. 
description: # Telomere Profiling Dataset: Telomere dataset used for calculating bulk
 and chromosome specific telomere lengths
 [https://doi.org/10.5061/dryad.dz08kps5d](https://doi.org/10.5061/dryad.dz08kps5d) The dataset includes demultiplexed raw telomere reads that were used for measuring telomere length across a wide population, telomere reads from the HG002 cell line, as well as custom CHM13 and HG002 reference genomes with truncated telomere sequences which were used for mapping reads. ## Description of the data and file structure 1\) Data files types are described in the table below. | **Data Type** | **File Name** | **Description** | **Additional info** | | :-------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Telomere reads from individual donors.  | JHIDXX.FXX.NBXX.fastq | JHID=individual donor number, F=experiment number, NB=barcode used | Each file contains telomere reads (fastq) from a single donor. Age of donor can be found in Table S2 of manuscript. Barcode sequence can be found in Table S3. The dataset includes telomere sequences from 132 individual donors and 15 donors diagnosed with short telomere syndromes. JH173-JH191 represent samples from short telomere syndrome patients.  | | Intra-assay variance data. | IntraRunXX.F52.NBXX.fastq | 14 total files reflecting a single source sample ligated and prepared using different barcodes and sequenced on a single flow cell. | Barcode sequence can be found in Table S3. | | Inter-assay variance data. | InterRunXX.F20.NBXX.fastq | 6 data files reflecting single source material which was sequenced on 6 different flow cells.  | Barcode sequence can be found in Table S3. | | Inter lab variance data.  | JHXX.UCSC.A24MixX.NBXX.fastq, or JHIDXX.FXX.NBXX.fastq | 14 data files reflecting samples prepared and sequenced by different people at UCSC or Johns Hopkins. UCSC file names include: JHID=individual donor ID number, UCSC marker, Mix=experiment number, NB=barcode. Samples sequenced at Hopkins include JHID=individual donor ID number. F=experiment number, NB=barcode number | Barcode sequence can be found in Table S3. | | Customized reference genomes with removed telomeres used for mappings | 1) HG002.v0.7.TeloBP.cut.XXX.fasta ; 2) GCA\_009914755.4\_T2T-CHM13v2.0\_genomic.TeloBPBoundaries.500kb.ends.fna | The last 500kb of subtelomere sequence from chromosome arms of the HG002 or CHM13 genomes were used to create a customized reference for telomere length measurements using mapping software. Telomeres were removed using the TeloBP algorithm. For HG002 three reference genomes are included for Only Paternal haplotype (denoted Paternal), Only Maternal alleles (denoted Maternal), or both combined in a single file (denoted Both). | TeloBP algorithm can be found at GitHub.com/GreiderLab | | HG002 sequenced telomeres | HG002.1AXX.NBXX.fastq.gz | Telomeres sequenced from HG002 cell line. A=experiment number. NB=barcode. | Alignment based pipeline for calculating telomere length of HG002 dataset can be found at GitHub.com/GreiderLab |