|
| Status |
Public on Mar 22, 2021 |
| Title |
iPSC_1 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell/tissue type: Undifferentiated iPSC (MHHi001-A)
age: passage 20 (on feeder) + 7 (monolayer)
batch number: -
growth protocol: Undifferentiated cells generated and cultivated as described (Haase et al. 2017 Stem Cell Res.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent and purified through sodium-acetate precipitation.
200 ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
N1635
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt
|
| Data processing |
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (version 1.3). Sequenced reads were trimmed for adaptor sequence (Trim Galore! 0.5.0), the reads were aligned (STAR2.6.1d) and RNA reads were assigned and counted (featureCounts1.6.4). Report was generated by MultiQC1.7.
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table” which was set to “Yes”.
Genome_build: Homo sapiens; Reference data coming from GENCODE (www.gencodegenes.org); Genome sequence (GRCh38.p12) - Release 29 (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/GRCh38.primary_assembly.genome.fa.gz); Comprehensive gene annotation (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz).
Supplementary_files_format_and_content: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt: Tab-delimited text file includes RPKM values for each Sample.
|
| |
|
| Submission date |
Mar 17, 2020 |
| Last update date |
Mar 22, 2021 |
| Contact name |
Monika Szepes |
| Organization name |
Hannover Medical School
|
| Department |
Department of Cardiac, Thoracic, Transplantation and Vascular Surgery
|
| Lab |
Leibniz Research Laboratories for Biotechnology and Artificial Organs
|
| Street address |
Carl-Neuberg Str. 1
|
| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE147122 |
Polysaccharide-based scaffolds for in situ hydrogelation: Use for next generation of bioartificial cardiac tissues |
|
| Relations |
| BioSample |
SAMN14391844 |
| SRA |
SRX7939715 |
