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Sample GSM624686 Query DataSets for GSM624686
Status Public on Feb 26, 2011
Title HeLa-PASSeq
Sample type SRA
 
Source name HeLa cell
Organism Homo sapiens
Characteristics cell line: HeLa
Growth protocol HeLa cells were grown in DMEM plus 10% fetal bovine serum or FetalPlex (Gemini). Mouse C57BL/6NTac ES cells were a kind gift of Thomas Fielder from the Transgenic Mouse Facility at UCI. Mouse fetal-derived neural stem/progenitor cells (NSPCs) were isolated from cerebral cortical regions of wild-type CD1 mice at embryonic day 12.5 (E12.5) and neurons were derived from the same set of E12.5 mouse cortices.
Extracted molecule polyA RNA
Extraction protocol PAS-Seq: PolyA+ RNAs are fragmented to 60-200nt pieces. Reverse transcription is performed using the Clontech SMART system using Superscript III. After second strand synthesis, cDNAs are size-selected and amplified by PCR. A custom primer is used for sequencing on Solexa Genome Analyzer II.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
 
Description PAS-Seq
cDNA sequence upstream of poly(A) junctions
Data processing mRNA-SEQ reads were retrieved GERALD (Generation of Recursive Analysis Linked by Dependency) the last step in the Illumina software. These reads were filtered by trimming Ts off the beginning reads and removing reads that have a string of 12 or more Ts. The remaining mRNA-SEQ reads were mapped to the human (hg18) and mouse genomes (mm9) allowing up to two mismatches using the aligner Bowtie version 0.12.6 with the settings “bowtie -m 1 --best -p 4”. Alignments due to potential internal priming were removed if a read has 6 or more consecutive As or 7 or more As in the 10 nucleotides immediately downstream of the poly(A) junction.
the file "GSE25450_hela_custom_track.txt" has the deep sequencing reads for the poly(A) sites in the hg18 format
 
Submission date Nov 17, 2010
Last update date May 15, 2019
Contact name Peter Shepard
E-mail(s) peter.shepard@gmail.com
Organization name University of California, Irvine
Department M&G
Lab Shi Lab
Street address Med Sci B233
City Irvine
State/province CA
ZIP/Postal code 92697-4025
Country USA
 
Platform ID GPL9052
Series (1)
GSE25450 RNA polyadenylation landscape in human and mouse cells
Relations
SRA SRX037422
BioSample SAMN00189613

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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