|
| Status |
Public on Aug 24, 2022 |
| Title |
XEN_hyp_d7_RNA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Extraembryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: --
condition: hypoxia d7
cell type: Extraembryonic stem cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, 74004). 500ng RNA was used as input for library preparacion.
Library preparation was performed using KAPA RNA HyperPrep Kit (Kapa Biosystems, KR1350) following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw reads were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --overlap 20 --minimum-length 25 --adapter "A[100]" --adapter "T[100]").
Reads were aligned to the mouse reference genome (mm10) using STAR (version 2.7.5a; parameters: --runMode alignReads --chimSegmentMin 20 --outSAMstrandField intronMotif --quantMode GeneCounts) and transcripts were assembled using StringTie (version 2.0.6; parameters: -e) with GENCODE annotation (VM19).
Table of read counts was generated using featureCounts function of the Rsubread package (version 1.32.4).
Transcripts Per Kilobase Million (TPM) was used to generate normalized expression values using EdgeR package (version 3.26.8).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text table containing TPM values per gene and sample for merged biological replicates
|
| |
|
| Submission date |
Jun 21, 2021 |
| Last update date |
Aug 24, 2022 |
| Contact name |
Natalia Lopez-Anguita |
| E-mail(s) |
anguita@molgen.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Department |
Genome Regulation
|
| Lab |
Bulut-Karslioglu Lab
|
| Street address |
Ihnestraße 63
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE178624 |
Hypoxia induces a transcriptional early primitive streak signature in pluripotent cells enhancing spontaneous elongation and lineage representation in gastruloids [RNA-seq] |
| GSE178628 |
Hypoxia induces an early primitive streak signature, enhancing spontaneous elongation and lineage representation in gastruloids |
|
| Relations |
| BioSample |
SAMN19801221 |
| SRA |
SRX11190716 |
