NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2481417 Query DataSets for GSM2481417
Status Public on Sep 19, 2017
Title Y4
Sample type SRA
 
Source name Decidua
Organism Homo sapiens
Characteristics tissue: Decidua
infection: HCMV
pool number: 2
time post infection: 1dpi
Extracted molecule total RNA
Extraction protocol Tissues were washed extensively, frozen and RNA was purified using M&N Nucleospin RNA purification kit according to the protocol.
RNA libraries were prepared for sequencing using standard Illumina TrueSeq protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Trimming the 51st position, then trimming the 3' end, using an in-house Perl script, with a quality threshold of 35.
Adapter sequences were removed using an in-house perl script allowing for up to 10% mismatches and requiring at least 6 bases overlap
The remaining reads were further filtered using the fastq_quality_filter program of the FASTX package (version 0.0.14) with a quality threshold of 30 in at least 95% of the read's positions.
The processed fastq files were mapped to the human genome GRCh37 using TopHat version 2.0.13 with Ensembl release 75 annotations. The following configuration was used: -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 20 --read-realign-edit-dist 4
Quantification, normalization and differential expression were done with the Cufflinks package (v2.2.1). Quantification was done with cuffquant, using the -b and -u parameters. Differential expression was calculated with cuffdiff, using default parameters.
 
Submission date Feb 09, 2017
Last update date May 15, 2019
Contact name Yiska Weisblum
E-mail(s) yiska.weisblum@mail.huji.ac.il
Organization name Hadassah Hebrew University Medical Center
Street address Kiryat Hadassah
City Jerusalem
ZIP/Postal code 91120
Country Israel
 
Platform ID GPL11154
Series (1)
GSE94724 Transcriptome analysis of HCMV infected tissues
Relations
BioSample SAMN06317460
SRA SRX2546934

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap