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| Status |
Public on Apr 02, 2019 |
| Title |
MAAC, 1week, rep1 |
| Sample type |
SRA |
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| Source name |
Adipose tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Adipose
sample type: MAAC, 1 week
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| Extracted molecule |
total RNA |
| Extraction protocol |
The adipose tissue was removed of fibrous material, finely minced, and digested in collagenase buffer containing HBSS +CaCl2+MgCl2 (Gibco 14065-49), 2% BSA, and 800U/g of tissue (~3mg/g of tissue) of type 2 collagenase (Worthington-LS004177) for approximately 40 min at 37°C. Digested material was passed through a 250 um strainer and washed 3 times with a total of 1L of KRHB buffer (1x KRH, 25mM HEPES, 2mM glucose, 2%BSA) using a separation funnel (VWR 527-0007) to separate the infranatant which contains the preadipocytes from the floating mature adipocytes.
RNA quality and quantity were assessed using a Fragment Analyzer standard sensitivity RNA kit (AATI # DNF-471) according to manufacturer’s instructions. Libraries were prepared using Illumina’s stranded total RNA library prep kit with “ribo-gold” rRNA depletion (catalog# RS-122-2303). The quality of the libraries were assessed using a Fragment Analyzer standard-sensitivity NGS kit (AATI # DNF-473). Samples were pooled so that they were present at an equal molarity. Pooled samples were sequenced 2x with NextSeq high output 150 cycle kits (Illumina # FC-404-2002), paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Hs_TW_1_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.
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| Data processing |
Quantification of the data was done using BCBIO version 1.0.1.
Hisat2 version 2.0.5 was used within BCBIO to align the data against the human hg38 assembly.
Sailfish 0.10.1 was used within BCBIO to quantify gene and exon counts.
Genome_build: hg38 (GRCh38) assembly
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw count values for each sample, along with Ensembl IDs and gene symbols.
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| Submission date |
May 29, 2018 |
| Last update date |
Apr 02, 2019 |
| Contact name |
Adil Mardinoglu |
| Organization name |
SciLifeLab, KTH
|
| Department |
Systems biology
|
| Street address |
Tomtebodavägen 23B
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| City |
Solna |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE115020 |
Culture of mature adipocytes under a permeable membrane and comparative analysis with different cell culture models |
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| Relations |
| BioSample |
SAMN09274998 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3163106_Hs_TW_1_wk_rep1.txt.gz |
514.4 Kb |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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