Published March 26, 2024
| Version v2
Dataset
Open
A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing
Authors/Creators
- 1. Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- 2. National Genomics Infrastructure hosted by Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- 3. Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
Description
This is a public repository containing secondary datasets described in the publication "A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing". Primary data for this project are available at NCBI/SRA under the BioProject accession numbers PRJNA600820 and PRJNA834955, and include the following sequencing datasets:
REH cell line:
- PacBio WGS
- ONT Ultralong WGS
- Illumina short-read PCR-free WGS
- IsoSeq RNA-seq
- Illumina short-read RNA-seq
GM12878 cell line:
- Illumina short-read RNA-seq
This dataset includes the following files:
Depth of Coverage analysis
- Output from `samtools coverage`: samtools.coverage.illumina.txt, samtools.coverage.ont.txt, samtools.coverage.pb.txt
- Output from `copycat` (binned coverage): copycat.ont.coverage.10kb.csv, copycat.pb.coverage.10kb.csv, copycat.pcrfree.coverage.10kb.csv
Structural Variant (SV) callsets
- Raw: illumina.tiddit.vcf, ont.sniffles.vcf, pb.sniffles.vcf
- Filtered: REH.svs.filtered.csv
SNV callsets
- Filtered and annotated: REH.mutect.filtered.ann.vcf.gz
Fusion gene callsets
- Short-read: GM12878.fusionreport.txt, illumina.all.txt, illumina.filtered.csv, REH.arriba.fusions.tsv, REH.fusioncatcher.fusion-genes.txt, REH.pizzly.txt, REH.squid.fusions.annotated.txt, REH.starfusion.abridged.tsv, REH.pdf
- Long-read: cupcake.long.csv, cupcake.std.csv, jaffa_results.csv
- Filtered: REH.fusions.filtered.csv
Files
copycat.ont.coverage.10kb.csv
Files
(434.1 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:3b5692dc779140b37acf460751c35bc2
|
10.2 MB | Preview Download |
|
md5:49e573d06b6f8662aef3a34bdde3004f
|
10.1 MB | Preview Download |
|
md5:aeebbfedaa9b1c59a64543358a3c59ab
|
10.2 MB | Preview Download |
|
md5:9c8669c640e6d83983ff07b64d7ad32b
|
1.5 MB | Preview Download |
|
md5:74ce21841a9b9d820c8189a43860e5e0
|
355.3 kB | Preview Download |
|
md5:bc011f8e4638455e51df063252064544
|
81.4 kB | Preview Download |
|
md5:d8b4dca5913a2d6414bc30a5cacaef43
|
80.9 kB | Preview Download |
|
md5:54c3c59a182ead9c65755b2c860ae4d4
|
2.1 kB | Preview Download |
|
md5:9c03030769ff09b9a27c8fcd9ef8794d
|
1.6 MB | Download |
|
md5:d3b92027bf5b16f6e6b11cf07e956e9a
|
921.9 kB | Preview Download |
|
md5:a9c2d1588d15ac05c351b3c1d2ac8cb4
|
18.0 MB | Download |
|
md5:d1d217bc0a1177f4141a8b9f073f3569
|
15.3 MB | Download |
|
md5:b9e1ee4e00803d1f049ec384390d6b57
|
45.9 kB | Download |
|
md5:33946bb9bf5fefc58f0b234167431b6c
|
2.7 MB | Preview Download |
|
md5:3dcf15397d14beb28ef6788165a121c9
|
33.4 kB | Preview Download |
|
md5:43182b90c96e90c69d07a64b38b55cc8
|
549.6 kB | Preview Download |
|
md5:b3bf5fc643cff842e7acfd2e82d3a6a7
|
357.5 MB | Download |
|
md5:06133c15889cec40f44be0104addf7b0
|
4.5 MB | Preview Download |
|
md5:a81d0f02b9409e29922f4772862940c4
|
34.0 kB | Preview Download |
|
md5:6fe85ed1f31d30bceed21e4f6bc7c3ae
|
2.3 kB | Download |
|
md5:2261ebff0e463c94a6b321570f822ca3
|
50.2 kB | Preview Download |
|
md5:3e52200cc6782d088e4a356e7a2bff52
|
145.0 kB | Preview Download |
|
md5:7e1a6d6816f498060e3a2c53602be7ee
|
27.4 kB | Preview Download |
|
md5:6d4d4871ac57a91c8826faa14a5094b4
|
27.2 kB | Preview Download |