|
| Status |
Public on Mar 12, 2024 |
| Title |
HSM1_T2_R1 |
| Sample type |
SRA |
| |
|
| Source name |
primary human skeletal muscle cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HSM1
timepoint: T2
treatment: no treatment
|
| Treatment protocol |
Cells were differentiatiated in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 2% horse serum. Samples were collected 1, 3, 5 and 7 days post treatment.
|
| Growth protocol |
Primary human skeletal muscle cells were cultivated in Hams F-10 with 20% Fetal Bovine Serum and basic Fibroblast Growth Factor (bFGF) at 37˚C until 80% confluent.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was harvested in Trizol and stored at -80˚C until Quant-seq analysis.
The Library was made using Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD according to the manufacturer's instructions, which was then sequenced on Illumina HiSeq 3000.
Sequencing was by the MHTP Medical Genomics Facility and applied Illumina directional RNA-seq on the Illumina Hiseq3000 using 150bp forward read. Libraries were purifified using AMPureXp beads and QC’d by Qubit, Bioanalyzer and qPCR. Mean size 343bp; 7.8nM.
[Cluster Generation] c-bot clustering using 200pM of library pool. Illumina Protocol 15006165 v02 Jan 2016
[Sequencing Chemistry] PE sequencing using Illumina HiSeq 3000. Illumina Protocol 15066493 Rev A, February 2015
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 2000 bases down-strand of a gene are counted towards that gene. Total reads per gene and reads with a poly(A) tail per gene are tabulated.
Genome_build: Homo sapiens ensembl version 93
Supplementary_files_format_and_content: genewise-count.csv contains counts of reads aligning to each gene and peakwise-count.csv contains counts of reads aligning to each peaks called by the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools).
|
| |
|
| Submission date |
Mar 15, 2021 |
| Last update date |
Mar 12, 2024 |
| Contact name |
Akriti Varshney |
| E-mail(s) |
akriti.varshney@monash.edu
|
| Organization name |
Monash University
|
| Street address |
Wellington Rd
|
| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE168897 |
Alternative polyadenylation is a minor feature of primary human muscle differentiation |
|
| Relations |
| BioSample |
SAMN18310902 |
| SRA |
SRX10340517 |
