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Status |
Public on Oct 10, 2018 |
Title |
antagomiR-122+CL4 |
Sample type |
SRA |
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Source name |
Liver
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 treatment: antagomiR-122 and CL316243 tissue: liver
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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.
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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
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
every sample represent one mouse
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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.
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Submission date |
Oct 11, 2016 |
Last update date |
May 15, 2019 |
Contact name |
chofit chai |
E-mail(s) |
chofit.chai@mail.huji.ac.il
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Organization name |
hadassah
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Department |
gene therapy
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Street address |
Ein Karem
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City |
Jerusalem 9112001 |
ZIP/Postal code |
9112001 |
Country |
Israel |
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Platform ID |
GPL19057 |
Series (1) |
GSE87848 |
RNA-seq analysis of livers of C57BL/6 mice upon antagomiR-122 and CL316243 treatment |
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Relations |
BioSample |
SAMN05896742 |
SRA |
SRX2239006 |
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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