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Sample GSM2498225 Query DataSets for GSM2498225
Status Public on Feb 13, 2019
Title adipocyte_control_rep1
Sample type SRA
Source name adipocyte
Organism Homo sapiens
Characteristics tissue: adipose
shRNA treatment: control
Treatment protocol ASC-adipocytes were transduced on day 8 post adipogenic induction with either control shRNA or linc-ADAL shRNA in a 6-well plate scale.
Growth protocol Primary human adipose stromal cells (ASCs) were extracted from freshly isolated subcutaneous adipose tissue and expanded in DMEM/F-12 medium supplemented with 10% fetal bovine serum and human EGF and FGF. For adipocyte differentiation, confluent ASC (passage 5-10) were incubated in differentiation media containing insulin (1.7 μM), dexamethasone (250 nM), isobutylmethylxanthine (500 μM), PPARγ agonist GW347845 (2 μM), panthothenate (4 mg/L) and biotin (8 mg/L). After 7 days, cells were incubated with medium supplemented with insulin (1.7 μM), dexamethasone (250 nM), panthothenate (4 mg/L) and biotin (8 mg/L) for additional 7 days.
Extracted molecule polyA RNA
Extraction protocol RNA samples were extracted using Trizol (Invitrogen) according to the manufacturer's instructions. Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA)
With a minimum of 1 µg input RNA, 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 TruSeq Stranded RNA Library Prep Kit (Illumina, San Diego, CA). Fragments of ~350 bp were selected by gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using Illumina’s HiSeq 2000.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) read was uniquely mapped, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp
Differential expression was tested by Cuffdiff with options "-u ". Annotation included mRNAs from RefSeq and stringent set of lincRNAs from Cabili et al. 2011.
Genome_build: hg19
Supplementary_files_format_and_content: DIFF files were obtained from Cuffdiff output.
Supplementary_files_format_and_content: adipocyte_ctrl_shR.diff contains differential expression result for control v.s. linc-AQPEP KD. Annotation included mRNAs from RefSeq and stringent set of lincRNAs from Cabili et al. 2011. sample_1 = control, sample_2 = KD
Submission date Feb 22, 2017
Last update date May 15, 2019
Contact name Chenyi Xue
Organization name Columbia University
Street address 630 W 168th St.
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platform ID GPL11154
Series (1)
GSE95173 Human Long Intergenic Noncoding RNA Linc-ADAL Knockdown in Mature Adipocytes using Lentiviral ShRNA
BioSample SAMN06368561
SRA SRX2581591

Supplementary file Size Download File type/resource 160.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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