|
| Status |
Public on Aug 10, 2021 |
| Title |
WTC11 iPSCs - RNA-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
human iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: WTC11 iPSCs
cell line: WTC11
|
| Growth protocol |
WTC11 iPS cells were cultured on Matrigel-coated (Corning, 354277) plates with Essential 8™ Medium (Life Technologies, A1517001). WTC11 iPSCs were passaged using Accutase (STEMCELL Technologies, 07922) and 10 μM ROCK inhibitor Y-27632 (STEMCELL Technologies, 72302).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from fresh cells using the RNeasy Plus Mini Kit (Qiagen, 74134).
Approximately 1000 ng of extracted RNA was used to prepare libraries for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020594).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed to 51bp before aligning to hg38 genome assembly using STAR (v2.7.2b) with ENCODE recommended parameters
Gene expression levels (FPKM) were calculated using RSEM rsem-calculate-expression (v1.3.1) with gencode.v32 as annotation
TMM normaliztion of FPKM was performed by edgeR v3.24.3
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of averaged FPKM values across samples
|
| |
|
| Submission date |
Feb 16, 2021 |
| Last update date |
Aug 10, 2021 |
| Contact name |
Yin Shen |
| E-mail(s) |
Yin.Shen@ucsf.edu
|
| Phone |
4155023403
|
| Organization name |
UCSF
|
| Department |
Department of Neurology
|
| Lab |
Shen Lab
|
| Street address |
513 Parnassus Ave
|
| City |
SAN FRANCISCO |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94143-0410 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE166837 |
Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [RNA-seq] |
| GSE166839 |
Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath |
|
| Relations |
| BioSample |
SAMN17925154 |
| SRA |
SRX10109400 |
