Dataset Open Access

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

Freeberg, Mallory; Heydarian, Mohammad

The data provided here are part of a Galaxy tutorial that analyzes RNA-seq data 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 chromosome 19 and a subset of interesting genomic loci identified by Wu et al.

Files (2.1 GB)
Name Size
G1E_R1_forward_downsampled_SRR549355.fastqsanger.gz
md5:6e2560e20eaf13669d8f2e80bafa9cc6
366.7 MB Download
G1E_R1_reverse_downsampled_SRR549355.fastqsanger.gz
md5:ba869c7bb379f0100b0a480f0d7478d5
344.7 MB Download
G1E_R2_forward_downsampled_SRR549356.fastqsanger.gz
md5:b2c13994f8b8d89e0cae3995ec866a96
442.9 MB Download
G1E_R2_reverse_downsampled_SRR549356.fastqsanger.gz
md5:e203f8b9b15577d8b5da99915f5b718d
416.8 MB Download
Megakaryocyte_R1_forward_downsampled_SRR549357.fastqsanger.gz
md5:dfad86456728be9ac8f3a9e20ab84f9a
266.4 MB Download
Megakaryocyte_R1_reverse_downsampled_SRR549357.fastqsanger.gz
md5:eea2bcc306c4d194f0e01a7ae8f710fe
250.8 MB Download
Megakaryocyte_R2_forward_downsampled_SRR549358.fastqsanger.gz
md5:34ff65fa309549803355bab59427a0ba
16.3 MB Download
Megakaryocyte_R2_reverse_downsampled_SRR549358.fastqsanger.gz
md5:83119917df4f6284b405ab288580dada
15.4 MB Download
RefSeq_gene_annotations_mm10.bed.gtf.gz
md5:e16d89fc7e88cf36420503b5058f3827
5.0 MB Download
RNAseq_regions_of_interest.bed.gz
md5:a1b30fce42d658cceafe059c9f064a11
525 Bytes 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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