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Sample GSM4953889 Query DataSets for GSM4953889
Status Public on Dec 07, 2020
Title BV2_KD_C2
Sample type SRA
 
Source name BV2 cells
Organism Mus musculus
Characteristics treatment: Scrambled control of PU.1 knock-down
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_KD.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 SAMN16983105
SRA SRX9621118

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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