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Sample GSM5567674 Query DataSets for GSM5567674
Status Public on Nov 10, 2021
Title C1_HEK_148_E5_S49
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 SAMN21357729
SRA SRX12105386

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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