DOI: 10.5281/zenodo.17055095
title: De novo alignments of RNA-seq for human cell lines reported in PMID:36638328, now unavailable

description: Introduction

This dataset contains genomic alignments and derived results generated de novo from RNA-seq data that accompanied an article and was made public by the authors. The motivation for these alignments was to examine claims in the article much more directly than is feasible with standard expression results.

Many RNA-seq data sets deposited in the same archive as these reads are diligently and systematically re-analyzed by  the Ma'ayan Lab (for human and mouse samples - see ARCHS4) and by NCBI staff (for human samples; explanation, example). Although the samples in this experiment were human cell lines, it appears that neither set of results was generated, presumably as a consequence of an unusual choice mentioned in the article:



The data generated in this study are publicly available at Sequence Read Archive with Accession: PRJNA822231.


This data was not associated with a GEO series. In addition, the reads are no longer in SRA, but the associated records are:



No public data is linked to this project.(...)


 




Title


KDM6A Loss Triggers an Epigenetic Switch That Disrupts Urothelial Differentiation and Drives Cell Proliferation in Bladder Cancer



Authors
Hong Qiu, Vladimir Makarov, Jennifer K Bolzenius, Angela Halstead, Yvonne Parker, Allen Wang, Gopakumar V Iyer, Hannah Wise, Daniel Kim, Varna Thayaparan, Daniel J Lindner, Georges-Pascal Haber, Angela H Ting, Bing Ren, Timothy A Chan, Vivek Arora, David B Solit, Byron H Lee


Journal & issue
Cancer Res. 2023 Jan 13;83(6):814–829


DOI
10.1158/0008-5472.CAN-22-1444


Pubmed
36638328


RNA-seq samples
human cell lines RT4, SCaBER, SW780




 
description: Methods

Corresponding genome and transcriptome reference files were obtained from Ensembl (GRCh38, release 109). Reads were aligned with STAR version 2.7.11a. Gene counts were obtained with featureCounts version 2.0.1. The samtools suite version 1.21 was used to sort BAM files and create CRAM files. Figures were generated with IGV and a modified version of Trackplot that reduces introns to a fixed length and displays splice junctions on the same quantitative scale as exons (i.e., with their peaks corresponding to their counts).
description: Contents

CRAM files are provided individually to facilitate the verification of results. Gene counts and alignments for KDM6A are provided as separate files (text and figures, respectively).

The scripts used for every step (except for figures) are included in files.zip, along with the combined and individual outputs of featureCounts.



files:├── counts_combined.txt├── gene.bams.realigned.zip├── gene.bams.zip├── KDM6A_counts.html├── KDM6A_counts.txt├── figures│   ├── KDM6A_IGV.2.png│   ├── KDM6A_IGV.png│   ├── trackplot.KDM6A.RT4.png│   ├── trackplot.KDM6A.SCaBER.png│   └── trackplot.KDM6A.SW780.png├── counts│   ├── RT4_KO_1.bam.counts.log│   ├── RT4_KO_1.bam.counts.txt│   ├── RT4_KO_1.bam.counts.txt.summary│   ├── ...│   └── SW780_par_2.bam.counts.txt└── scripts_and_logs    ├── bams_to_crams_human.sh    ├── get_genomic_refs_human.sh    ├── build_genomic_refs_human.sh    ├── gene_refs_human.sh    ├── coords_from_gtf.py    ├── combine_counts.py    ├── combine_counts.human.sh    ├── abra2.sh    ├── fastq.files.txt    ├── star.commands.and.manifests.zip    └── star.outputs.and.logs.zip


 

 
description: KDM6A expression




sample    
KDM6A counts


RT4_KO_1
2048


RT4_KO_2
2242


RT4_par_1
2742


RT4_par_2
2302


SCaBER_KO_1
1166


SCaBER_KO_2
1094


SCaBER_par_1
4307


SCaBER_par_2
2946


SW780_KO_1
3233


SW780_KO_2
3732


SW780_par_1
5148


SW780_par_2
5955