|
| Status |
Public on Aug 19, 2019 |
| Title |
M70 |
| Sample type |
SRA |
| |
|
| Source name |
subcutaneous white adipose tissue
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Subcutaneous adipose tissue-derived mesenchymal progenitor cells
clone_number: 70
condition: M
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using NucleoSpin RNA XS kit (Clontech Laboratories Inc. Cat. No. 740902). Briefly, cells were detached as mentioned in previous section, snap frozen in liquid nitrogen and stored at -80oC overnight. Next day, RNA was prepared from a total of 168 samples across three conditions (C, M and F) according to the manufacturer’s instructions.
cDNA library was prepared using SMART-Seq v4 3’ DE kit according to the manufacturer’s instructions (Clontech Laboratories Inc. Cat. No. 635040). For each clone, 1 ng of total RNA was used as input to synthesize cDNA which was subsequently amplified. Control RNA was provided with the kit. All samples were processed concurrently during library preparation. Prior to purification, the amplified cDNA’s were grouped in fourteen pools of twelve samples each with a unique barcode (Clonetech Oligo dT in-line indexes or IL 1-12) ligated to the 3’end during cDNA synthesis. Pooled and purified libraries were fragmented using Nextera XT DNA Sample Preparation Kit (Illumina, Cat. Nos. FC-131-1024, FC-131- 1096). Illumina sequencing indexes (provided with the SMART-Seq v4 3’ DE kit) were added to the fragmented libraries and indexed libraries were amplified. For intermittent purification steps, Agencourt AMPure XP PCR purification kit (5 ml Beckman Coulter Part No. A63880; 60 ml Beckman Coulter Part No. A63881) was used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: TPM.txt
|
| Data processing |
The FASTQ files obtained were de-multiplexed using SMART-Seq DE3 Demultiplexing Software by Clontech.
Bowtie was used to align the reads to the human genome assembly hg19.
The aligned reads were then processed by RSEM to generate un-normalized and TPM counts.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TPM.txt: Tab-delimited text file includes TPM values for each sample.
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Aug 19, 2019 |
| Contact name |
Silvia Corvera |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Massachusetts Medical School
|
| Street address |
373 Plantation St
|
| City |
Worcester |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE134570 |
Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells |
|
| Relations |
| BioSample |
SAMN12324088 |
| SRA |
SRX6476738 |
