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Sample GSM3743855 Query DataSets for GSM3743855
Status Public on Jun 08, 2020
Title NPC_HD_Rep2_RNA-seq
Sample type SRA
 
Source name Neural progenitor cells
Organism Macaca mulatta
Characteristics cell type: Neural progenitor cells
disease state: Huntington’s Disease
Extracted molecule total RNA
Extraction protocol The RNA was extracted using Qiagen miRNeasy Mini Kit with DNase digestion. The RNA quantity and quality were validated using Nanodrop 2000 Spectrophotometer and Agilent’s 4200 Bioanalyzer Capillary electrophoresis.
Amplified mRNA was fragmented, and barcodes were added using Illumina’s Nextera XT kits. Amplified Libraries were validated by Agilent 4200 Tapestation and quantified using a Qubit fluorimeter. Libraries were normalized, pooled and clustered on an Illumina HiSeq 3000/4000 Flowcell using the Illumina cBOT. The libraries were sequenced on an Illumina HiSeq 3000 system in 101-base single-read reactions with multiplexing to achieve approximately 20 million reads per sample. RNA-seq experiments were performed in three different replicates.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing ATAC-seq raw reads were trimmed using pyadapter_trim.py.
Reads were aligned to the “MacaM_Rhesus_Genome_Annotation_v7.8.2” genome using Tophat2 v2.1.0 with the flags, “--no-mixed –no-discordant” for RNA-seq, and using bowtie version 2 2.2.6 with the flag, “-X 2000” for ATAC-seq.
Non-uniquely mapped reads were excluded from both RNA-seq and ATAC-seq samples, and duplicates were removed from ATAC-seq samples using picard-tools-2.1.7 MarkDuplicates.
For ATAC-seq, only fragments < 115 bp in length were kept, as those indicate transcription factor binding.
.bam files were converted to .bed using “bamToBed -split” for RNA-seq, and .bedpe using “bamToBed -bedpe” for ATAC-seq. The ATAC-seq .bedpe file was converted to a bed file containing only the beginning and end of each fragment.
.bed files were converted to bedGraph using “bedtools genomecov -scale”, where the scale factor was the total number of uniquely mapped reads for RNA-seq, and the total number of uniquely mapped, non-duplicate fragments for ATAC-seq. The result is an RPM-normalized .bedGraph file for each replicate. .bedGraph files were then converted to bigwig using “bedGraphToBigWig”
Genome_build: MacaM_Rhesus_Genome_Annotation_v7.8.2
Supplementary_files_format_and_content: bigwig files of RPM-normalized signal.
 
Submission date May 01, 2019
Last update date Jun 10, 2020
Contact name Isaac Kremsky
E-mail(s) ikremsk@emory.edu
Organization name Emory University
Department Biology
Lab Corces
Street address 1510 Clifton Rd
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platform ID GPL23804
Series (1)
GSE130570 Chromatin Accessibility and Transcription Dynamics During In Vitro Astrocyte Differentiation of Huntington’s Disease Monkey Pluripotent Stem Cells.
Relations
BioSample SAMN11552742
SRA SRX5775603

Supplementary file Size Download File type/resource
GSM3743855_HD_NPC_R2.merged.UM.sorted.bw 86.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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