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Sample GSM1128651

Query DataSets for GSM1128651

Status

Public on Jul 12, 2013

Title

A_adipose_postLPS (Sample 2)

Sample type

SRA

Source name

adipose_postLPS

Organism

Homo sapiens

Characteristics

tissue: adipose
treatment: LPS

Extracted molecule

total RNA

Extraction protocol

For adipose tissue, the RNA was extracted using RNeasy lipid total RNA mini kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA). Poly-A library preparation and RNA sequencing were performed at the Penn Genome Frontiers Institute’s High-Throughput Sequencing Facility per Illumina’s (San Diego, CA) standard protocols. Briefly, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the Illumina paired-end sample preparation kit. Fragments of ~350 bp were selected gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using Illumina’s HiSeq 2000 at four lanes per sample (~456 million to 701 million 2 × 101 bp paired-end reads per sample).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Generate gene expression by cufflink v1.3.0
Generate alternative splicing files by MATS2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: Standard cufflink outputs, tab-delimited text files including FPKM values and FDR adjusted p-values.
Supplementary_files_format_and_content: A_adipose_gene_exp.xls contains the differentially expressed genes from cuffdiff at variant read depths. The read depths were ranged from 5M reads to 500M reads (full set). In the excel file one tab has the cuffdiff result for one read depth, e.g. adipose_100M indicates the differentially expressed gene results for adipose tissue at read depth 100M reads.
Supplementary_files_format_and_content: A_adipose_gene_exp_simluation_100M.xls contains the differentially expressed genes for certain read depth (100M reads here) for 10 times simulation. The purpose is to evaluate sampling variations and to see whether the sequenced reads are representative. Each tab in the excel file contains the differentially expressed genes for each simulation rounds, as a result, 10 tabs in this file. Similar description for A_adipose_gene_exp_simulation_10M.xls file, the only difference is the read depth in simulation is 10M reads.
Supplementary_files_format_and_content: MATS_A_adipose.xls represents the alternative-splicing (AS) results from Multivariate Analysis of Transcript Splicing (MATS). Similar to A_adipose_gene_exp.xls, it contains the AS results for adipose tissue at variant depths from 5M to 500M reads. Each tab represents the AS results for one depth.
Supplementary_files_format_and_content: MATS_A_adipose_simulation_100M.xls and MATS_A_adipose_simulation_10M.xls represents the AS results for 10 times simulation at read depths 100M and 10M reads. Similar to A_adipose_gene_exp_simulation_100M.xls and A_adipose_gene_exp_simulation_10M.xls, each tab contains the AS result for one simulation rounds, as a result, totally 10 tabs.

Submission date

Apr 23, 2013

Last update date

May 15, 2019

Contact name

Yichuan Liu

Organization name

University of Pennsylvania

Street address

423 Guardian Drive

City

Philadelphia