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Sample GSM2570067 Query DataSets for GSM2570067
Status Public on May 02, 2017
Title HeLa_500ng_PACSeq
Sample type SRA
 
Source name HeLa Cells in culture
Organism Homo sapiens
Characteristics cell line: HeLa
treatment: mock
dilution: 500ng
Treatment protocol New samples are PACseq libraries of serially diluted samples of the same original sample of HeLa total cellular RNA. Serial dilutions were performed to establish the minimal requirement for starting RNA in PACseq.
Extracted molecule total RNA
Extraction protocol TRIzol Extraction from cells in culture
Poly(A)-ClickSeq (PAC-seq) libraries where generated using oligo-dT primers carrying partial p7 Illumina adaptors in RT-PCR reactions supplemented with azido-terminating nucleotides (AzVTPs). Azido-blocked cDNAs covering the junction of the 3'UTR and poly(A) tails were thus generated and were 'click-ligated' to p5 Illumina sequencing adaptors using the 'ClickSeq' methodology. These cDNA libraries were amplified by PCR to fill-in the Indexing sequences and the rest of the p7 adaptor.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Data processing CASAVA or MiSeq Reporter demultiplexing
Custom trimming and filitering to remove poly(A) tails (See Routh et al)
Mapping of processed reads to hg19 with HiSat2
Custom Scripts to extract poly(A) site and frequency (see Routh et al)
Genome_build: hg19
Supplementary_files_format_and_content: BEDGraph (4 tab-delimted columns: chromosome number \t start coordinate \t end coordinate \t read count)
 
Submission date Apr 06, 2017
Last update date May 15, 2019
Contact name Zheng Xia
E-mail(s) xiaz@ohsu.edu
Organization name Oregon Health & Science University
Department Department of Biomedical Engineering
Lab Xia Lab
Street address 3181 SW Sam Jackson Park Rd
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
 
Platform ID GPL15520
Series (1)
GSE94950 Poly(A)-ClickSeq resolves CF25-mediated alternative poly-adenylation, HeLa
Relations
BioSample SAMN06697611
SRA SRX2730624

Supplementary file Size Download File type/resource
GSM2570067_HeLa_500ng_prep.f.bedgraph.gz 53.4 Kb (ftp)(http) BEDGRAPH
GSM2570067_HeLa_500ng_prep.r.bedgraph.gz 50.5 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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