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| Status |
Public on Feb 01, 2024 |
| Title |
SGBS_day11_rep10 (RNA-Seq) |
| Sample type |
SRA |
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| Source name |
SGBS cells at day 11 of adipocyte differentiation
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SGBS preadipocyte cell line
time: day 11
experiment: 2
replicate: 10
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| Growth protocol |
Human Simpson-Golabi-Behmel syndrome (SGBS) pre-adipocytes were grown to confluency in Dulbecco’s Modified Eagle’s Medium (DMEM)/F-12Nutrient Mixture (Ham) supplemented with 10 % fetal bovine serum (FBS), 33 µM biotin, 17 µM pantothenate, 100 U/ml penicillin, 100 µg/ml streptomycin, 1ng/µl fibroblast growth factor (FGF) 1, and 90 µg/ml heparin. Three days post-confluency (day 0), SGBS cells were washed three times with PBS and stimulated to differentiate with serum-free growth medium, supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM rosiglitazone/BRL49653, 500 µM 1-methyl-3-isobuthylxanthine (IBMX), 250 nM dexamethasone (Dex), and 0.01 mg/ml human transferrin. After 6 days, FGF-1, Heparin, IBMX, Dex, rosiglitazone were removed from the medium. Cells were harvested at day 0, 1, 7 and 11.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent (Sigma Aldrich) and the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions, including an DNAse I digest (RNase-free DNAse set, Qiagen) and Proteinase K digest (Puregene Proteinase K, Qiagen). RNA quality was checked by Agilent Bioanalyzer ( Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA).
Illumina TrueSeq Stranded total RNA Library Prep Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Day11_rep10
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| Data processing |
Data were processed with the nf-core rnaseq pipeline. Default parameters were used unless mentioned otherwise.
Sequences were aligned to the human reference genome (hg19/GRCh37) by application of the software HISAT2, with --unstranded option.
Transcripts were assembled using StringTie and gene codes gene annotation v.29 lift 37.
Gene counts were generated with the Stringties prepDE.py script (setting: -eb).
Normalized counts per million (CPM) were used for statistical analyses performed by edgeR.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: gene_count_matrix.csv (Raw gene count data in a comma-separated .csv file)
Supplementary_files_format_and_content: transcript_count_matrix.csv (Raw transcript count data in a comma-separated .csv file)
Supplementary_files_format_and_content: gene_logCPM_differential.txt (Log2CPM (LogCPM), mean (NormAve), standard error (SE_NormAve), log2 fold changes (logFC) and FDR values calculated with respect to SGBS at day 0 in a tab-delimited .txt file)
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| Submission date |
May 16, 2019 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Clarissa Feuerstein-Akgoz |
| Organization name |
DKFZ
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE131317 |
Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [RNA-Seq exp2] |
| GSE131318 |
Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers |
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| Relations |
| BioSample |
SAMN11658534 |
| SRA |
SRX5845124 |
| 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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