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| Status |
Public on Feb 13, 2019 |
| Title |
adipocyte_control_rep1 |
| Sample type |
SRA |
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| Source name |
adipocyte
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| Organism |
Homo sapiens |
| Characteristics |
tissue: adipose
shRNA treatment: control
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Feb 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chenyi Xue |
| Organization name |
Columbia University
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| Street address |
630 W 168th St.
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE95173 |
Human Long Intergenic Noncoding RNA Linc-ADAL Knockdown in Mature Adipocytes using Lentiviral ShRNA |
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| Relations |
| BioSample |
SAMN06368561 |
| SRA |
SRX2581591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2498225_adipocyte_c1.bw |
160.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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