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| Status |
Public on May 31, 2019 |
| Title |
High Fat Diet TSP1 Knockout Mice 1 |
| Sample type |
SRA |
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| Source name |
High Fat Diet TSP1 Knockout mice
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57/BL6
genotype/variation: TSP-1 Knockout
diet: CDAHFD
tissue: liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with Trizol (Thermo Fisher Scientific # 15596026) after tissue homogenization with Omni TH Tissue Homogenizer.
1 ug of RNA was used for cDNA library construction at Novogene using an NEBNext Ultra Directional RNA library Prep Kit for Illumina (cat# E7420S, New England Biolads, Ipswich, MA, USA) according to the manufacture's protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification, and fragmented randowmly by adding fragmentation bufffer. The first strand cDNA was synthesized using random hezamers primer, after which as custom second-strand synthesis biffer (Illumina), dNTPs, RNase H and DNA polymnerase I were added to generate the second-strand (ds cDNA). After a series of terminal repair, poly-adenylation, and sequencing adaptor ligation, the double-stranded cDNA library was completed following size selection and PCR enrichment. The resulting 250-350 bo insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Walthan, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Techmologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina, San Diego, CA, USA) using a paired-end 150 run (2x150 bases). 20M raw reads were generated from each library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
HFKO1
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| Data processing |
20 M 2x150 paired end reads were generated from an Illumina HiSeq 4000 Platform
Following raw reads were filtered: reads containing adaptors, reads containinng N>10% (N represents the base connot be determined); reads containing low quality (Qscore<=5) bases which is over 50% of the total reads.
QuickRNASeq pipeline was used in reads mapping and counting: STAR 2.5.2.a was used for mapping; featureCounts subread-1.5.1 was used for counting; RSeQC was used for read QC; VarScan.v2.4.0 was used for SNP calling.
Genome_build: Genome fasta file is GRCh38.primary.genome.fa. Gene annotation file is GRCh38.gencode v25 annotation file. Gtf file is GRCh38.gencode.v25.gtf; Bed file is GRCh38.gencode.v25.bed
Supplementary_files_format_and_content: Processed data is a tab delimited text file contains gene name as row, and the fpkm for that gene from each sample is the column.
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| Submission date |
Oct 09, 2018 |
| Last update date |
May 31, 2019 |
| Contact name |
Ju Wang |
| E-mail(s) |
[email protected]
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| Phone |
+1 (617) 6747453
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| Organization name |
Pfizer Inc
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| Department |
Inflammation & Immunology
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| Street address |
610 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE120977 |
Transcriptomic analysis of liver mRNA from TSP-1 KO and WT mice fed with normal diet or choline deficient amino acid defined diet (CDAHFD, human NASH model) |
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| Relations |
| BioSample |
SAMN10220722 |
| SRA |
SRX4815900 |
| 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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