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Sample GSM6758331 Query DataSets for GSM6758331
Status Public on Jan 31, 2024
Title CTRL2.D14_S2
Sample type SRA
 
Source name Cultures of in vitro differentiated primary subcutaneous human adipocytes
Organism Homo sapiens
Characteristics tissue: Cultures of in vitro differentiated primary subcutaneous human adipocytes
condition: CTRL
Treatment protocol Once differentiated, we challenged these cultures of primary human adipocytes with the ectopic presence of synthetic small interfering (si-)RNAs directed against our lncRNA candidate or a non-targeting si-RNA control.
Growth protocol To induce the adipogenic conversion of adipocyte progenitors, human preadipocytes (SP-F-1, Zen-Bio, Inc.) were led to grow as a monolayer in preadipocyte medium (PM-1) until reaching confluence, and then incubated with adipocyte differentiation medium (DM-2) for 7 days. This media is composed of DMEM / Ham’s F-12 (1:1), HEPES, FBS, biotin, pantothenate, insulin, dexamethasone, IBMX, PPARγ agonist, penicillin, streptomycin and amphotericin B. Thereafter, differentiating adipocytes were maintained in adipocyte maintenance medium (AM-1) for 7 additional days (DM-2 without dexamethasone, IBMX and PPARγ agonists). During this process, the shape of preadipocytes evolves from the flattened form to rounded cells containing abundant lipid droplets, and are thus considered differentiated, mature adipocytes (~12th day and thereafter).
Extracted molecule polyA RNA
Extraction protocol Total RNA was purified from human adipose tissue and cells using RNeasy Mini Kit (QIAgen, 74104). Fat samples (~150 µg) and cell monolayers were homogenized in 0.6 mL of QIAzol® Lysis Reagent (QIAgen, 79306).
NGS libraries with polyA capture were prepared according to the manual Protocol for use with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) (versión 1.0, 4/17)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description CTRL2.D14_S2
Data processing Human: Raw sequencing reads in the fastq files were mapped with STAR version 2.7.1a to the Gencode release 36 based on the GRCh38.p12 reference human genome with the corresponding GTF files.
Table counts was obtained with FeatureCounts function in the package subread, version 1.6.4
Assembly: GRCh38
Supplementary files format and content: txt files containing the table counts obtained with FeatureCounts
 
Submission date Nov 28, 2022
Last update date Jan 31, 2024
Contact name Júlia Perera-Bel
E-mail(s) mardata-bu@researchmar.net
Organization name Hospital del Mar Research Institute
Department MARData-BU
Street address Doctor Aiguader, 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL18573
Series (2)
GSE218896 A new adipocyte-specific long non-coding RNA engages impaired fatty acid sensing and dyslipidaemia in obese subjects (RNA-seq)
GSE218897 Functional consequences of impaired linc-GALNTL6-4 in adipocytes
Relations
BioSample SAMN31891924
SRA SRX18397933

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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