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Browsable TIF-Seq2 tracks from K562 after imatinib treatment

dataset
posted on 03.12.2020, 12:54 by Vicent Pelechano, Jingwen Wang, bingnan Li, Sueli Marques
Browsable dataset containing transcript boundaries for the manuscript:

Jingwen Wang, Bingnan Li, Sueli Marques, Lars M Steinmetz, Wu Wei, Vicent Pelechano, TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes, Nucleic Acids Research, Volume 48, Issue 18, 09 October 2020, Page e104, https://doi.org/10.1093/nar/gkaa691

The alignment files contains sequences of K562 cells using TIF-Seq2 method. The sequencing reads were aligned to the human reference genome hg38. Each read pair represents the boundary of an individual transcript. The first reads in pairs are 5' ends, while the second reads in pairs are 3' ends. The alignment files can be loaded into IGV for visualization. You can set up view as pairs in the alignment track.

Source code for the associated manuscript is available from GitHub at https://github.com/jingwen/TIFseq2

Raw data is deposited at GEO with access code GSE140912

Funding

Impact of transcriptome complexity on gene expression dynamics

Swedish Research Council

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Wallenberg Academy Fellowship [KAW 2016.0123]

Swedish Foundations’ Starting Grant (Ragnar Söderberg Foundation)

Karolinska Institutet (SciLifeLab Fellowship, SFO and KI funds)

National Key R&D Program of China [2017YFC0908405]

National Natural Science Foundation of China [81870187]

US National Institutes of Health [NIH grant P01 HG000205]

Deutsche Forschungsgemeinschaft [1422/4-1]

European Research Council Advanced Investigator Grant

Joint China-Sweden mobility grant from STINT [CH2018-7750]

National Natural Science Foundation of China [81911530167]

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Karolinska Institutet

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