|
| Status |
Public on Jan 11, 2019 |
| Title |
P1_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 |
| E-mail(s) |
[email protected]
|
| 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 |
|
| Relations |
| BioSample |
SAMN10175293 |
| SRA |
SRX4796915 |
