|
| Status |
Public on May 02, 2017 |
| Title |
HeLa_125ng_PACSeq |
| Sample type |
SRA |
| |
|
| Source name |
HeLa Cells in culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: mock
dilution: 125ng
|
| 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 |
SAMN06697613 |
| SRA |
SRX2730622 |
