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Sample GSM7078405 Query DataSets for GSM7078405
Status Public on Oct 31, 2023
Title RNA_cortex_WT_rep1
Sample type SRA
 
Source name cortex
Organism Mus musculus
Characteristics tissue: cortex
cell line: cortex-neuron
cell type: neuron
genotype: wildtype
Extracted molecule polyA RNA
Extraction protocol 1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
Total RNA from culture cells was extracted using Trizol reagents (Life Technologies) following the manufacturer’s instructions. Total mRNA was prepared from 1 mg total RNA using poly(A) mRNA magnetic isolation reagents (NEB) and fragmented at 94 °C for 15 min. RNA was then reverse-transcribed into cDNA with random primers. After end repairing and A-tailing, cDNA was ligated with adapters and amplified by PCR with Illumina sequencing primers.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.
Supplementary files format and content: GSE225162
 
Submission date Mar 02, 2023
Last update date Oct 31, 2023
Contact name Xiao Ge
Organization name Shanghai JiaoTong University
Street address No. 800 Dongchuan Road
City Shanghai
ZIP/Postal code 200240
Country China
 
Platform ID GPL24247
Series (2)
GSE210817 Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation
GSE225162 Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation [RNA-seq]
Relations
BioSample SAMN33574226
SRA SRX19554132

Supplementary file Size Download File type/resource
GSM7078405_RNA_cortex_WT_rep1.fpkm_tracking.gz 857.1 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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