|
| Status |
Public on Dec 03, 2019 |
| Title |
LPM1G1 |
| Sample type |
SRA |
| |
|
| Source name |
engineered lateral mesoderm cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hPSC-derived lateral mesoderm
es line: H9
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cultures using RNeasy mini from Qiagen. DNA contamination was removed from the samples using DNA-free™ DNA Removal Kit from Ambion (Thermofisher).
cDNA synthesis and Illumina libraries were performed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit from TAKARA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence with Trim Galore version: 0.4.1 (a wrapper for Cutadapt 1.8.1 with parameters -f fastq -e 0.1 -q 20 -O 1 and FastQC)
Reads were mapped to GRCh38 whole genome using HiSAT2 v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Counts were produced using SeqMonk 0.34. All reads overlapping an exon were counted, all reads from all exons of all isoforms added, counting each one once.
Counts Per Million reads (CPM) were calculated dividing reads from all exons of all isoforms by the size of the library in reads, multiplied by 1 million.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma Separated Value file containing Counts Per Million reads. Rows are genes (rownames are Gene Symbols) and columns are cells.
|
| |
|
| Submission date |
Nov 21, 2018 |
| Last update date |
Dec 03, 2019 |
| Contact name |
Nicolas Gambardella |
| E-mail(s) |
nicolas@ascistance.co.uk
|
| Phone |
00447833147074
|
| Organization name |
aSciStance Ltd
|
| Street address |
Lewis House, Great Chesterford Court
|
| City |
Great Chesterford |
| State/province |
Essex |
| ZIP/Postal code |
CB10 1PF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE122827 |
BNC1 is a master regulator of human epicardial cell heterogeneity and function |
|
| Relations |
| BioSample |
SAMN10461018 |
| SRA |
SRX5054282 |
