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Series GSE61332 Query DataSets for GSE61332
Status Public on Apr 23, 2015
Title Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution
Organism Homo sapiens
Experiment type Other
Expression profiling by high throughput sequencing
Summary Major features of transcription by human RNA polymerase II (Pol II) remain poorly defined due to a lack of quantitative approaches for visualizing Pol II progress at nucleotide resolution. We developed a simple and powerful approach for performing native elongating transcript sequencing (NET-seq) in human cells that globally maps strand-specific Pol II density at nucleotide resolution. NET-seq exposes a mode of antisense transcription that originates downstream and converges on transcription from the canonical promoter. Convergent transcription is associated with a distinctive chromatin configuration and is characteristic of lower-expressed genes. Integration of NET-seq with genomic footprinting data reveals stereotypic Pol II pausing coincident with transcription factor occupancy. Finally, exons retained in mature transcripts display Pol II pausing signatures that differ markedly from skipped exons, indicating an intrinsic capacity for Pol II to recognize exons with different processing fates.
Overall design 10 samples were analyzed. NET-seq data for HeLa S3 cells consisted in 2 WT biological replicates (HeLaS3_Rep1 and HeLaS3_Rep2), 1 treatment condition (HeLaS3_FP) and 1 control for the treatment condition (HeLaS3_DMSO). NET-seq data for HEK293T cells consisted in 2 WT biological replicates (HEK293T_Rep1 and HEK293T_Rep2). RNA-seq data for HeLa S3 cells consisted in the 3 cellular fractions in WT condition (HeLaS3_chromatin_RNAseq, HeLaS3_nucleoplasm_RNAseq and HeLaS3_cytoplasm_RNAseq). RNA-seq data for HEK 293T cells consisted in the cytoplasmic fraction in WT condition (HEK293T_cytoplasm_RNAseq)
Contributor(s) Churchman LS
Citation(s) 25910208
Submission date Sep 11, 2014
Last update date May 15, 2019
Contact name Stirling Churchman
Organization name Harvard Medical School
Department Genetics
Street address 77 Avenue Louis Pasteur
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (10)
GSM1505438 NET-seq HeLa S3 Rep2
GSM1505439 NET-seq HeLa S3 Rep1
GSM1505440 NET-seq HEK293T Rep1
BioProject PRJNA261235
SRA SRP047174

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Supplementary file Size Download File type/resource
GSE61332_RAW.tar 1.2 Gb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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