Dataset Open Access

Training data for de novo transcriptome reconstruction from RNA-seq data

Heydarian, Mohammad; Freeberg, Mallory; Poterlowicz, Krzysztof

The data provided here are part of a Galaxy Training Network tutorial that analyzes RNA-seq data using a de novo transcriptome reconstruction strategy from a study published by Wu et al., 2014 (DOI:10.1101/gr.164830.113). The goal of this study was to investigate "the dynamics of occupancy and the role in gene regulation of the transcription factor Tal1, a critical regulator of hematopoiesis, at multiple stages of hematopoietic differentiation." To this end, RNA-seq libraries were constructed from multiple mouse cell types including G1E - a GATA-null immortalized cell line derived from targeted disruption of GATA-1 in mouse embryonic stem cells - and megakaryocytes. This RNA-seq data was used to determine differential gene expression between G1E and megakaryocytes and later correlated with Tal1 occupancy. This dataset (GEO Accession: GSE51338) consists of biological replicate, paired-end, polyA selected RNA-seq libraries. Because of the long processing time for the large original files, we have downsampled the original raw data files to include only reads that align to a subset of interesting genomic loci identified by Wu et al. This dataset represents an even smaller set of data than another training data set (DOI:10.5281/zenodo.254485).

Files (1.7 GB)
Name Size
G1E_rep1_forward_read_(SRR549355_1)
md5:712324a599eb08c509f63e1879ddbdb0
277.3 MB Download
G1E_rep1_reverse_read_(SRR549355_2)
md5:8c71b47a480f6dad38b64861df1653ec
277.3 MB Download
G1E_rep2_forward_read_(SRR549356_1)
md5:6cd4c921b4aee906289dc2c741d548a2
362.2 MB Download
G1E_rep2_reverse_read_(SRR549356_2)
md5:b504e15f427a7e8dfd35b46842b44196
362.2 MB Download
Megakaryocyte_rep1_forward_read_(SRR549357_1)
md5:535b73ef414bfd7412d8439518c671d7
213.4 MB Download
Megakaryocyte_rep1_reverse_read_(SRR549357_2)
md5:e48cc6b9582804870602a5689bfa23b9
213.4 MB Download
Megakaryocyte_rep2_forward_read_(SRR549358_1)
md5:888f80ec68222e4789148b06cce83ec1
12.7 MB Download
Megakaryocyte_rep2_reverse_read_(SRR549358_2)
md5:285f5fe45a4633ec71ae33dc60115782
12.7 MB Download
RefSeq_reference_GTF_(DSv2)
md5:93f6c98b78ec49b2c24fa528ab1677ca
427.4 kB Download
  • Afgan, E et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. 44, W3-W10 (2016).
  • Wu, W et al. Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. 24, 1945-1962 (2014).
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