|
| Status |
Public on Oct 28, 2021 |
| Title |
Organoids Day 30, wild-type, 12uM CHIR Repeat #1 - RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
WIBR3 hESC Choroid plexus Organoids
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: Organoids Day 30
genotype: Wild type
cell line: WIBR3
treatment: 12uM CHIR
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from samples using RNEASY mini-kit (Qiagen)
RNA libraries were prepared for sequencing using bulk MARS-seq protocol [Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types Science 343, 776–9 (2014).] and TruSeq stranded mRNA library kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
counts_chir_RNAseq.txt
CHIR41_S0_L009
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg38 whole genome using Cutadapt -a $adapter -q 20 fastqf ($adapter= sequence of adapter Fastqf= fastqfile) and STAR.
Raw counts were processed, and normalized reads were obtained by DESeq2.
Genome_build: GRCh37/hg38
Supplementary_files_format_and_content: tab-delimited text files include read values for each sample.
|
| |
|
| Submission date |
Dec 07, 2020 |
| Last update date |
Oct 28, 2021 |
| Contact name |
Orly Reiner |
| E-mail(s) |
orly.reiner@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Molecular Genetics
|
| Lab |
Orly Reiner
|
| Street address |
234, Herzl Street,
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE162808 |
MARS Seq and total RNA seq data from human choroid plexus organoids |
|
| Relations |
| BioSample |
SAMN17018888 |
| SRA |
SRX9642734 |
