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Sample GSM2341906 Query DataSets for GSM2341906
Status Public on Oct 10, 2018
Title antagomiR-cont+CL4
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics strain: C57BL/6
treatment: antagomiR-control and CL316243
tissue: liver
Treatment protocol C57BL/6 mice were tail vain injected with 5 µg/mice antagomiR-122 or antagomiR-control, 48 hours later they were injected s.c with 1mg/kg CL316243, 2 hours later they were sacrificed.
Growth protocol Male C57BL/6 mice, 7-8 weeks old, were purchased from Harlan Laboratories (Jerusalem, Israel). All mice were kept in a pathogen-free facility, under a 12 h light/dark cycle
Extracted molecule total RNA
Extraction protocol Livers were removed, frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description every sample represent one mouse
Data processing base-calling with bcl2fastq (v2.15.0.4), default parameters
quality-trimming at both ends, using in-house Perl scripts, with a quality threshold of 32.
adapter removal with cutadapt (version 1.7.1), using parameters -O 1, --match-read-wildcards and -m 15.
filtering by quality with fastq_quality_filter of the FASTX package (version 0.0.14), using parameters -q20 and -p 90.
Alignment with TopHat (v2.0.13), using parameters -G Ensembl_78_genes.gtf, -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 20, --read-realign-edit-dist 2, --coverage-search and –microexon-search.
Quantification, normalization and differential expression were done with the Cufflinks package (v2.2.1). cuffquant using parameters -b, -u and -M; cuffdiff using default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file, where the first 14 columns are gene details (according to column headers), next are FPKM values per each sample (as computed with Cufflinks), next are cuffdiff results for comparing antagomiR-122 to antagomiR-cont samples.
 
Submission date Oct 11, 2016
Last update date May 15, 2019
Contact name chofit chai
E-mail(s) chofit.chai@mail.huji.ac.il
Organization name hadassah
Department gene therapy
Street address Ein Karem
City Jerusalem 9112001
ZIP/Postal code 9112001
Country Israel
 
Platform ID GPL19057
Series (1)
GSE87848 RNA-seq analysis of livers of C57BL/6 mice upon antagomiR-122 and CL316243 treatment
Relations
BioSample SAMN05896738
SRA SRX2239002

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

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