|
| Status |
Public on Dec 31, 2023 |
| Title |
hESC derived neurons, Control, Biol Rep 2 [C_02] |
| Sample type |
SRA |
| |
|
| Source name |
H9
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: embryonic stem cells
treatment: No treatment
|
| Treatment protocol |
On day 49, the neurons were treated with cis-RSV and trans-RSV (50 mM each) for a period of 24 hours, followed by collection of cell pellet in ice-cold PBS, using cell scrapers, to obtain cell pellet for RNA extraction.
|
| Growth protocol |
Human embryonic stem cell (hESCs) line H9 was used to differentiate human cortical neurons.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extract by Zymo Quick-RNA MicroPrep Kit and cleaned by Zymo RNA Clean and Concentrator Kit. 0.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext dA tailling and Ultra II Directional RNA Library prep Kit(E#7600) following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text files include gene counts for each sample
|
| |
|
| Submission date |
Mar 12, 2023 |
| Last update date |
Dec 31, 2023 |
| Contact name |
HAO JI |
| E-mail(s) |
ji5@email.sc.edu
|
| Phone |
8037774689
|
| Organization name |
University of South Carolina
|
| Department |
College of Pharmacy
|
| Street address |
715 SUMTER ST CLS RM 109
|
| City |
COLUMBIA |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE227181 |
cis-RSV and trans-RSV have differential effects on gene transcription in human embryonic stem cells derived neurons |
|
| Relations |
| BioSample |
SAMN33730770 |
| SRA |
SRX19645465 |
