|
| Status |
Public on Dec 07, 2020 |
| Title |
BV2_OE_C2 |
| Sample type |
SRA |
| |
|
| Source name |
BV2 cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Empty frame control of mouse PU.1 overexpression
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
The BV2 cells were cultured in DMEM (Gibco #11965) supplemented with 5% heat-inactivated fetal bovine serum (FBS, Gibco #16140) and 100 U/ml penicillin-streptomycin (Pen/Strep, Gibco #15140).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was extracted with RNeasy mini kit (QIAgen #74106) including the DNase I treatment step with RNase-Free DNase set (QIAgen #79254) according to manufacturer’s instructions.
Libraries were prepared using TruSeq RNA Sample Prep Kit v2 and sequenced using Illumina HiSeq 2500 with 100-bp single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Spi1_OE.tsv
|
| Data processing |
Base-calling was performed with Illumina Casava 1.8.2 software, and demultiplexing was performed using Illumina bcl2fastq Conversion Software v2.18.
Sequence reads were aligned to the mouse reference genome of UCSC mm10 using STAR (v2.5.2a) with default parameters and soft clipping enabled.
Read counts of genes were estimated by featureCounts with default parameters.
Differential gene expression was analyzed in DESeq2 (v1.14) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files of sample CPM values (counts per million; i.e the raw counts divided by library size in millions).
|
| |
|
| Submission date |
Dec 02, 2020 |
| Last update date |
Dec 07, 2020 |
| Contact name |
Alison Goate |
| E-mail(s) |
alison.goate@mssm.edu
|
| Phone |
212-659-5672
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Department of Genetics and Genomic Sciences
|
| Street address |
Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE162526 |
Alzheimer’s-associated PU.1 expression levels regulate microglial inflammatory response |
|
| Relations |
| BioSample |
SAMN16983099 |
| SRA |
SRX9621125 |
