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Sample GSM7040348 Query DataSets for GSM7040348
Status Public on Oct 31, 2023
Title RNA_f_del_rep1
Sample type SRA
 
Source name cortex
Organism Mus musculus
Characteristics tissue: cortex
cell line: cortex-neuron
cell type: neuron
genotype: CBSf del -/-
Extracted molecule total 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.
 
Submission date Feb 13, 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 SAMN33269841
SRA SRX19351783

Supplementary file Size Download File type/resource
GSM7040348_RNA_f_del_rep1.fpkm_tracking.gz 851.6 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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