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Status |
Public on Jun 08, 2020 |
Title |
NPC_HD_Rep2_RNA-seq |
Sample type |
SRA |
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Source name |
Neural progenitor cells
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Organism |
Macaca mulatta |
Characteristics |
cell type: Neural progenitor cells disease state: Huntington’s Disease
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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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.
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Submission date |
May 01, 2019 |
Last update date |
Jun 10, 2020 |
Contact name |
Isaac Kremsky |
E-mail(s) |
ikremsk@emory.edu
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Organization name |
Emory University
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Department |
Biology
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Lab |
Corces
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Street address |
1510 Clifton Rd
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City |
Atlanta |
State/province |
GA |
ZIP/Postal code |
30322 |
Country |
USA |
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Platform ID |
GPL23804 |
Series (1) |
GSE130570 |
Chromatin Accessibility and Transcription Dynamics During In Vitro Astrocyte Differentiation of Huntington’s Disease Monkey Pluripotent Stem Cells. |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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