Flow sorted chromosome libraries, chromosome 19 of Homo sapiens: CHM1... - SRA

SRX14137770: Flow sorted chromosome libraries, chromosome 19 of Homo sapiens: CHM13 Expt 2
1 ILLUMINA (Illumina HiSeq 2500) run: 36.2M spots, 10.9G bases, 5.8Gb downloads

Design: Chromosomes were labeled for 2 hours with 50 g/ml Chromomycin A3 and 5 g/ml Hoechst 33258 in the presence of 25 mM sodium sulfite, 10 mM sodium citrate and 10 mM MgSO4. Before sorting, chromosome suspension was filtered through an 8 m strainer. Chromosomes were sorted on a MoFlo Legacy (Beckman Coulter) at 60-65 psi using a 70 m tip. Hoechst 33258 was excited with a UV laser (330-360nm) and the emission was detected in the 409-480 nm range. Chromomycin A3 was excited with the second laser tuned to 458 nm and emission was detected in a 505-605 nm range. Clumps and debris were excluded by gating on forward scatter versus pulse width (fig. S33). Chromosomes were sorted into DNA LoBind collection tubes (Eppendorf). Approximately 37000-123000 sorted events were collected per chromosome. Data analysis was performed using FlowJo (BD Life Sciences).Genomic DNA was extracted from sorted chromosomes using the MagAttract HMW DNA Kit (Qiagen). DNA was analyzed and quantified using a FemptoPulse (Agilent). Whole-chromosome shotgun libraries were prepared from one nanogram DNA using the Accel-NGS 2S DNA Library Kit (Swift Biosciences) with unique dual index adapters according to manufacturers protocol with the substitution of Kapa HiFi HotStart Ready Mix (Roche) for library amplification. Twelve cycles of PCR were used for samples with 2 ng DNA input and 15 cycles were used for the sample with 0.17 ng input DNA. The libraries were pooled for sequencing on a HiSeq 2500 DNA sequencer in Rapid mode (Illumina, Inc.), generating 336 M paired-end 151 bp reads.

Submitted by: UCSC Genomics Institute (UCSC GI)

Study: T2T - CHM13

PRJNA559484 • SRP219631 • All experiments • All runs

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We have sequenced the CHM13hTERT human cell line on the Oxford Nanopore GridION. We have also sequenced approximately 50x coverage using 10X Genomics as well as BioNano DLS and Arima Genomics HiC. PacBio data for this cell line has been previously generated by the Washington University School of Medicine and the University of Washington, and is available from NCBI SRA.Human genomic DNA was extracted from the cultured cell line. As the DNA is native, modified bases will be preserved. We followed Josh Quick's ultra-long read (UL) protocol for library preparation and sequencing.

Sample: Human sample from CHM13htert cell line from Homo sapiens

SAMN03255769 • SRS798661 • All experiments • All runs

Organism: Homo sapiens

Library:

Name: HM7LHBCX2_18806590_S3_L002

Instrument: Illumina HiSeq 2500

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 36.2M spots, 10.9G bases, 5.8Gb

Run	# of Spots	# of Bases	Size	Published
SRR17981961	36,162,591	10.9G	5.8Gb	2022-02-11

ID:: 19933972

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