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Sample GSM2420396 Query DataSets for GSM2420396
Status Public on Aug 06, 2019
Title HPV16_4
Sample type SRA
 
Source name Uterine cervix tumor
Organisms Homo sapiens; Human papillomavirus 16
Characteristics tissue: Uterine cervix tumor
hpv-type infection: HPV16
histological tumor classification: Squamous cell carcinoma
Treatment protocol All biopsies were collected before patient treatment and stored in RNAlater (Qiagen) at -80°C until mRNA isolation.
Growth protocol CaSki was grown in RPMI medium with 10% fetal bovine serum (Gibco) and 5% CO2.
Extracted molecule total RNA
Extraction protocol DNA and RNA were isolated from each sample and cell line with Qiagen AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. DNA and RNA were quantified and stored at -20°C and -80°C, respectively.
Libraries were prepared with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's recommendations.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava1.8 software used for basecalling.
Reads with low quality scores (Q < 20 phred score), short reads with lengths < 30 nucleotides, and reads with a high fraction of base ambiguities (> 60% ambiguous bases) were discarded using PRINSEQ.
To analyze likely integration events, a de novo transcriptome construction was carried out with Trinity. Subsequently, to identify chimeric transcripts, assembled transcript sequences were compared to the HPV genomic sequence with Blast tools to obtain high-scoring segment pairs (HSPs) with e-values < 1x10-6 and identity score ≥ 98%. Selected transcripts were additionally compared to the human genome (HG38) using Blast online to identify the Human/HPV chimeric transcripts.
The abundance of different HPV transcripts in cervical cancer samples was estimated by comparing HPV reads from each sample with corresponding HPV16 or HPV18 reference sequences (GenBank K02718.1 and AY262282.1, respectively) with BowTie 2 default settings. To analyze the expression of alternative E6 and E7 transcripts, reference sequences were initially constructed (HPV16_E6E7SJ.fasta and HPV18_E6E7SJ.fasta files) for each likely transcript.
Genome_build: K02718.1 (HPV16), AY262282.1 (HPV18), hg18 (human)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with counts of reads covering each nucleotide from the HPV genome.
Supplementary_files_format_and_content: Fasta files from chimerics contigs obtained from de novo assembly and blast selection. Fasta files constructed to analyse HPV16 and HPV18 E6/E7 alternative transcripts.
 
Submission date Dec 08, 2016
Last update date Aug 06, 2019
Contact name Ayslan Castro Brant
E-mail(s) ayslanbrant@gmail.com
Phone +55 21 3207-6561
Organization name National Institute of Cancer
Department Genetics
Lab Genetics
Street address Andre Cavalvanti 37
City Rio de Janeiro
State/province Rio de Janeiro
ZIP/Postal code 20231-050
Country Brazil
 
Platform ID GPL22767
Series (1)
GSE91065 Human Papillomavirus (HPV) genomic integration, expression and E6/E7 splicing patterns in cervical cancer associated with HPV16 or HPV18 infection
Relations
BioSample SAMN06126964
SRA SRX2407561

Supplementary file Size Download File type/resource
GSM2420396_HPV16_4_chimTrans.fasta.gz 667 b (ftp)(http) FASTA
GSM2420396_HPV16_4_depthcouter.txt.gz 27.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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