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Sample GSM7730721 Query DataSets for GSM7730721
Status Public on Oct 31, 2023
Title RNA_CBS3_KO_sample1_rep2
Sample type SRA
 
Source name cultured cell
Organism Homo sapiens
Characteristics tissue: cultured cell
cell line: HEK 293T cell line
cell type: Human embryonic kidney 293T
genotype: CBS3 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 Aug 23, 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 GPL24676
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 SAMN37125202
SRA SRX21468556

Supplementary file Size Download File type/resource
GSM7730721_RNA_CBS3_KO_sample1_rep2.fpkm_tracking.gz 1.4 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA

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