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| Status |
Public on Jan 01, 2018 |
| Title |
ML-2 |
| Sample type |
SRA |
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| Source name |
adult marmoset liver tissue
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| Organism |
Callithrix jacchus |
| Characteristics |
tissue: adult liver
age: 5-10 years
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of marmoset liver progenitor cell line and adult liver tissue was harvested using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
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 HiSeq 2500 |
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| Description |
Processed data file: fpkm.txt
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| Data processing |
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 100 bp/50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Reference genome and gene model annotation files were downloaded from genome website ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/. Index of the reference genome was built using Bowtie v2.0.6 and single-end clean reads were aligned to the reference genome using TopHat v2.0.9. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Genome_build: Homo sapiens Ensembl Release 84
Supplementary_files_format_and_content: fpkm.xls: Excel file includes FPKM values for all six Samples.
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| Submission date |
May 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
zhenglong guo |
| E-mail(s) |
zhenglongguo@zzu.edu.cn
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| Organization name |
Henan Provincial People's Hospital
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| Street address |
NO.7, Weiwu road
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| City |
Zhengzhou |
| State/province |
Henan |
| ZIP/Postal code |
450000 |
| Country |
China |
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| Platform ID |
GPL21580 |
| Series (1) |
| GSE99168 |
Transcriptomes analysis of marmoset liver progenitor cell line compared with adult marmoset liver |
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| Relations |
| BioSample |
SAMN07152235 |
| SRA |
SRX2840960 |
| 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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