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Sample GSM2160044

Query DataSets for GSM2160044

Status

Public on May 18, 2019

Title

DM2

Sample type

SRA

Source name

Decidua

Organism

Homo sapiens

Characteristics

tissue: Decidua
pool number: 2
time post infection: 2dpi
infection: Mock

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 protocols for the Nextseq library construction

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

processed data file: DESeq2_normc_dec.csv
DM2_S7

Data processing

The NextSeq basecalls files were converted to fastq files using bcl2fastq version 2.15.0.4 with default parameters.
Raw reads were quality-trimmed at both ends, using in-house Perl scripts, with a quality threshold of 32.
Adapter sequences were removed using cutadapt version 1.7.1 with parameters -O 1 --match-read-wildcards -m 15
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 20 in at least 90% of the read's positions.
The processed fastq files were mapped to the human genome GRCh38 using TopHat version 2.0.14 with Ensembl release 78 annotations. The following configuration was used: -N 3 --read-gap-length 5 --read-edit-dist 10 --segment-length 20 --read-realign-edit-dist 3
Quantification of raw counts per gene was done using cuffquant (cufflinks version 2.2.1) with parameters -b -u -M (masking for genes of type IG, TR, rRNA, tRNA, miRNA, snRNA, snoRNA, lincRNA and misc_RNA).
Raw counts were obtained by running cuffnorm on the cuffquant output.
Normalization and differential expression were done with DESeq2 version 1.6.3, for each tissue separately, while filtering out genes with a total of less than 2 counts in all samples, and using default parameters. The significance threshold was set to padj<0.1
Differential expression results were combined with gene details taken from BioMart (Ensembl, release 78).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values

Submission date

May 19, 2016

Last update date

May 18, 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