|
| Status |
Public on Aug 26, 2020 |
| Title |
S1KO48_CT0.4_D4 |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human ES-derived neural progenitor cells
cell line: H9
genotype: SOX1-/-
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from cells collected at different time points using TRIzol Reagent (Invitrogen). Isolated RNA was enriched by Poly(A) tails and fragmented. Sequencing libraries were prepared according to Illumina manufacturer instruction. Paired-end RNA-seq of 2x100 base pair reads were sequenced on Illumina Hiseq2000 platform or 2x150 base pair reads were sequenced on Hiseq X-ten
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7
Sequences are aligned to transcriptome with Salmon (v0.8.2)
Transcripts Per Million were calculated by Salmon(v0.8.2)by defalut parameters
Genome_build: hg38
Supplementary_files_format_and_content: comma seprated file(.csv) include TPM values for all samples
|
| |
|
| Submission date |
Sep 30, 2019 |
| Last update date |
Aug 26, 2020 |
| Contact name |
Zhuoqing Fang |
| Organization name |
Stanford
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE138217 |
SOX1 Determines the Regional Identity of Neural Progenitors Differentiated from Human Embryonic Stem Cells |
| GSE138218 |
SOX1 is required for the specification of rostral hindbrain neural progenitor cells from human embryonic stem cells |
|
| Relations |
| BioSample |
SAMN12876869 |
| SRA |
SRX6927357 |
