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Sample GSM3416375 Query DataSets for GSM3416375
Status Public on Jan 11, 2019
Title P4_Adipose_1
Sample type SRA
Source name Adipose tissue
Organism Homo sapiens
Characteristics tissue: Adipose
Treatment protocol hASC-derived adipocytes were treated with rosiglitazone for 48h beginning at day 21
Growth protocol hASCs at passage P3-P4 were cultured in DMEM medium. Confluent hASCs were then transferred into adipogenic medium for 14 days. Then, cells were further cultured in maintenance medium another 7 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by using Qiagen RNeasey Mini kit. Ribosomal RNA was depleted by Ribo-Zero gold kit.
DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier.
RNA libraries were prepared for sequencing using TruSeq RNA Sample Prep Kit. ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing ChIP-seq reads were aligned to human reference genome (hg19) using Bowtie2. Only unique mapped reads were considered for further analysis. Aligned reads from biological replicates were pooled together and peak calling was performed by HOMER with normalized tag count >=6, p value < 0.00001 and fold change >= 4 for each patient. After that peaks from each patient were merged together using BEDTools, and then resized to 200 bp.
RNA-seq reads were aligned to human reference genome (hg19) using Hisat2 with default parameters. Only unique mapped reads were considered for further analysis. Normalized expression value, fragments per kilobase of exon per million reads mapped (FPKM), was calculated for each gene using StringTie
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using HORMER V4.9; Normalized abundance measurement was generated using StringTie.
Submission date Oct 04, 2018
Last update date Jan 11, 2019
Contact name Chunjie Jiang
Phone 2153164211
Organization name University of Pennsylvania
Department Institute for Diabetes, Obesity, and Metabolism
Lab Mitchell A. Lazar
Street address 3400 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL24676
Series (1)
GSE115421 Patient adipose stem cell-derived adipocytes reveal genetic variation that predicts anti-diabetic drug response
BioSample SAMN10175287
SRA SRX4796921

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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