|
| Status |
Public on Nov 10, 2021 |
| Title |
C1_HEK_148_F3_S37 |
| Sample type |
SRA |
| |
|
| Source name |
cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: In vitro
tissue: single cell
cell line: 293T
|
| Growth protocol |
The human embryonic kidney 293T cell line was cultured in suspension in a DMEM medium supplemented 10% fetal bovine serum and 1% antibiotics (L-Glutamine-penicillin-streptomycin).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Recovered cells were centrifuged at 600g for 5 min and subsequently processed according the Fluidigm C1 Quick Reference User Guide (ID: PN 100-5003 C1). cDNAs were generated per cell using the" SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System" (Cat. Nos. 635025 & 635026) according to the manufacturers recommended procedure. cDNA libraries were quantified using Qbit and size distribution assessed via Fragmentanalyzer.
cDNAs obtained from each C1 Fluidigm chip were normalized for DNA concentration 0.3ng/ul. cDNA libraries were processed to obtain sequencing libraries using Nextera XT library prep kit (FC-131-1096) together with Nextera XT inxed kit 96 indexes set A (FC-131-2001) for each cell's cDNA. Sequencing libraries originated from one C1 Fluidigm chip were pooled and subsequently sequenced utilizing the NextSeq500.
Dual-indexed paired-end Illumina Nextera XT libraries (read1 = 16bp, read2 = 59bp)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were then sequenced on a NextSeq500 sequencer (Illumina) using paired-end run (read 1 - 16 bp, read 2 - 59 bp) with an average of 3 x 10^6 reads per library.
Read quality of sequenced libraries was evaluated with FastQC.
Sequencing reads were aligned to the reference human genome assembly GRCh38.90 using STAR (Dobin et al., 2013). Reads aligned to annotated genes were quantified with htseq-count (Anders et al., 2015).
Genome_build: GRCh38.90
Supplementary_files_format_and_content: tab-delimited text file include read-count matrices
|
| |
|
| Submission date |
Sep 08, 2021 |
| Last update date |
Nov 10, 2021 |
| Contact name |
Marjan Biočanin |
| E-mail(s) |
marjan.biocanin@epfl.ch
|
| Organization name |
EPFL
|
| Department |
SV-IBI
|
| Lab |
Laboratory for systems biology and genetics/UPDE
|
| Street address |
Station 19, SV 3820
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE148093 |
Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types |
| GSE183686 |
Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [C1-HEK] |
|
| Relations |
| BioSample |
SAMN21357739 |
| SRA |
SRX12105396 |
