|
| Status |
Public on Apr 14, 2023 |
| Title |
Donor 12455, 2mM EtOH, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
12455
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 12455
cell type: NGN2-induced neurons
genotype: WT
treatment: 7-Day 2mM EtOH Exposure
time: Day 28
|
| Treatment protocol |
Ethanol exposure began at 21 days post-induction, wither either 2 mM or 17 mM EtOH. EtOH was supplemented daily to account for evaporation.
|
| Growth protocol |
Doxycycline-inducible transcription factor NGN2 with puromycin selection and rt-TA lentiviruses were used on neural progenitor cells. After dox-induction and antibiotic selection, cells were grown in Neurobasal medium with B27 supplement up to 14 days post-induction, then transitioned to Neurobasal Plus medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
S12455_1__08_2
|
| Data processing |
Raw reads were assessed for quality using FastQC (version 0.11.8) before and after adapter sequence trimming by Cutadapt (version 4.1).
Reads were pseudoaligned using Salmon (version 0.13.1) for estimation of normalized gene expression (TPM, i.e. transcript per million).
Reads were also aligned to the human reference genome (Gencode version 28) and quantified for gene read counts, both in STAR (version 2.5.3a).
For differential gene expression analyses, read counts were modelled in the linear mixed model using batch, sex and donor information as the random effect terms and ethanol-treatment/control as the fixed effect term by the R (version 4.1.0) package "variancePartition" (version 1.28.0).
Assembly: hg38
Supplementary files format and content: "star_gene.tsv" includes reads counts for genes (in rows) across samples (in columns); "salmon_gene.tsv" includes TPM values for genes (in rows) across samples (in columns).
|
| |
|
| Submission date |
Mar 06, 2023 |
| Last update date |
Apr 14, 2023 |
| Contact name |
Paul Slesinger |
| E-mail(s) |
paul.slesinger@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neuroscience
|
| Street address |
1425 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE226746 |
Effect of 2 mM and 17 mM 7-day intermittent EtOH exposure on human excitatory neurons |
|
| Relations |
| BioSample |
SAMN33603222 |
| SRA |
SRX19577495 |
