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Status |
Public on Sep 19, 2017 |
Title |
Y3 |
Sample type |
SRA |
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Source name |
Decidua
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Organism |
Homo sapiens |
Characteristics |
tissue: Decidua infection: Mock pool number: 2 time post infection: 1dpi
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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.
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Submission date |
Feb 09, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Yiska Weisblum |
E-mail(s) |
yiska.weisblum@mail.huji.ac.il
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Organization name |
Hadassah Hebrew University Medical Center
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Street address |
Kiryat Hadassah
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City |
Jerusalem |
ZIP/Postal code |
91120 |
Country |
Israel |
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Platform ID |
GPL11154 |
Series (1) |
GSE94724 |
Transcriptome analysis of HCMV infected tissues |
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Relations |
BioSample |
SAMN06317461 |
SRA |
SRX2546933 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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