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Status |
Public on May 12, 2020 |
Title |
TAM_4days_WT_S15221 |
Sample type |
SRA |
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Source name |
primary liver
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 cell type: Liver genotype: WT treatment protocol: 4-OHT 20 mg/mg 4-OHT i.p. 4days
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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,
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
WT
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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
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Submission date |
Oct 02, 2019 |
Last update date |
May 12, 2020 |
Contact name |
Marco Filipuzzi |
E-mail(s) |
marco.filipuzzi@ieo.it
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Organization name |
IEO
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Street address |
Via Giuseppe Ripamonti, 435
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City |
Milan |
ZIP/Postal code |
20141 |
Country |
Italy |
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Platform ID |
GPL13112 |
Series (1) |
GSE138296 |
Cooperation of MYC and b-catenin in liver tumorigenesis requires Yap/Taz |
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Relations |
BioSample |
SAMN12889182 |
SRA |
SRX6935909 |
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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