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Sample GSM4104669 Query DataSets for GSM4104669
Status Public on May 12, 2020
Title TAM_4days_WT_S15219
Sample type SRA
 
Source name primary liver
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Liver
genotype: WT
treatment protocol: 4-OHT 20 mg/mg 4-OHT i.p. 4days
Treatment protocol For short-term liver-specific activation of the various alleles, 10^11 AAV8-TBG-CRE particles were given to 6- to 8-week-old mice and mice sacrificed after 4 days,
Extracted molecule total RNA
Extraction protocol Liver tissue was homogenized with GentleMACS M Tubes (Miltenyi Biotech, #130-096-335) and gentleMACS™ Dissociator (Miltenyi Biotech, #130-093-235) in RNA lysis buffer (Zymo, #R1054), and total RNA was purified from these lysates onto Quick-RNA Miniprep columns (Zymo, #R1054) and treated on-column with DNaseI. RNA quality was checked with the Agilent 2100 Bioanalyser (Agilent Technologies).
0.5-1 µg of RNA were used to prepare libraries for RNA-Seq with the TruSeq stranded total RNA Sample Prep Kit (Illumina, #20020596) following manufacturer instruction. RNA-seq libraries were then run on the Agilent 2100 Bioanalyser (Agilent Technologies) for quantification and quality control and then sequenced on Illumina NovaSeq or Illumina 2000 as detailed below.
Strand Specific RNA-Seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description WT
Data processing Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: txt file reporting the eRPKM, log2FC and padj from DESEq2 output
 
Submission date Oct 02, 2019
Last update date May 12, 2020
Contact name Marco Filipuzzi
E-mail(s) marco.filipuzzi@ieo.it
Organization name IEO
Street address Via Giuseppe Ripamonti, 435
City Milan
ZIP/Postal code 20141
Country Italy
 
Platform ID GPL13112
Series (1)
GSE138296 Cooperation of MYC and b-catenin in liver tumorigenesis requires Yap/Taz
Relations
BioSample SAMN12889184
SRA SRX6935907

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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