 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 17, 2020 |
| Title |
N1570_doxycycline control 2 |
| Sample type |
SRA |
| |
|
| Source name |
human iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSCs
treatment: control
genotype: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
iPSCs were harvested and RNA were isolated with miRNeasy mini kit (Qiagen). 500ng of total RNA was used for mRNA enrichment procedure with NEBNext PolyA mRNA magnetic Isolation Module.
Stranded cDNA library was generated using using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina with an additional purification step using Agencourt® AMPure® XP Beads. cDNA libraries were barcoded by dual indexing approach with NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422
nfcore/rnaseq (v1.3), pipeline: Nextflow (v18.10.1), FastQC (v0.11.8), TrimGalore (v0.5.0), STAR (vSTAR_2.6.1d), RSeQC (v3.0.0), dupRadar, Preseq (v2.0.3), featureCounts (v1.6.4), StringTie (v1.3.5), Sample_correlation, MultiQC (v1.7)
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: GRCh38; release 29
Supplementary_files_format_and_content: tab-delimited text files of raw read counts from each sample.
|
| |
|
| Submission date |
May 12, 2020 |
| Last update date |
Jun 18, 2020 |
| Contact name |
Christian Bär |
| E-mail(s) |
baer.christian@mh-hannover.de
|
| Phone |
00495115232883
|
| Organization name |
Hannover Medical School
|
| Department |
IMTTS
|
| Street address |
Carl-Neuberg-Str. 1
|
| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE150421 |
mRNA profiling after knockdown of lncRNA Cyrano |
|
| Relations |
| BioSample |
SAMN14906244 |
| SRA |
SRX8332880 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4550189_N1570.txt.gz |
292.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
