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| Status |
Public on Jan 31, 2024 |
| Title |
si.LINC2.D14.4_S8 |
| Sample type |
SRA |
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| Source name |
Cultures of in vitro differentiated primary subcutaneous human adipocytes
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Cultures of in vitro differentiated primary subcutaneous human adipocytes
condition: siLINC2
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| 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.
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| 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).
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
si.LINC2.D14.4_S8
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| 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
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| Submission date |
Nov 28, 2022 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Júlia Perera-Bel |
| E-mail(s) |
mardata-bu@researchmar.net
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| Organization name |
Hospital del Mar Research Institute
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| Department |
MARData-BU
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| Street address |
Doctor Aiguader, 88
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| 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 |
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| Relations |
| BioSample |
SAMN31891918 |
| SRA |
SRX18397939 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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