NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5419300 Query DataSets for GSM5419300
Status Public on Sep 15, 2021
Title Brd4-CUT&Tag in naïve CD8+T cells_rep2
Sample type SRA
 
Source name Naïve CD8+T cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Spleen-derived naive CD8+T cells
chip antibody: Brd4 (Active motif, AB_2615059, Catalog No 39910)
treatment: untreated
Extracted molecule genomic DNA
Extraction protocol Fifty-thousand isolated CD8+ T cells were used to generate CUT&Tag library as a reference[31]. First, CD8+ T cell was incubated with primary antibody against Brd4 (1:50; Active motif AB_2615059) and then with guinea pig anti-rabbit secondary antibody (1:100; Antibodies Online ABIN101961). This was followed by adding the prepared pA-Tn5 complex. Next, DNA was fragmented by Mg2+ activator and the resulting DNA segments were extracted to amplify with PCR. Finally, PCR products were cleaned up and sequenced. Paired-end 150-bp sequencing was performed on an Illumina HiSeq 2500. Each DNA library for CUT&Tag was sequenced with HiSeq 2500 system (Illumina, USA) under the paired-end 150 bp mode. For data processing, raw sequencing data were trimmed and filtered by using Trim Galore. The paired-end reads with high quality (Q30) were aligned to the mouse reference genome mm10 using the Burrows Wheeler Aligner with default parameters and then sorted using the SAMtools software. The “MarkDuplicates” function embedded in Picard was used to mark and discard PCR duplicates. For comparison between different samples, mapped reads were down-sampled to equalize reads across samples by using Samtools. MACS2 was used to quantify the Brd4 CUT&Tag signal throughout the genome and within gene bodies.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description BRD4Control_CD8_CutTag_BRD4_20210117_B1T2
Data processing library strategy:CUT&Tag-seq
Raw sequencing data were trimmed and filtered by using Trim Galore.
The paired-end reads with high quality (Q30) were aligned to the mouse reference genome mm10 using the Burrows Wheeler Aligner with default parameters and then sorted using the SAMtools software.
The “MarkDuplicates” function embedded in Picard was used to mark and discard PCR duplicates.
For comparison between different samples, mapped reads were down-sampled to equalize reads across samples by using Samtools. MACS2 was used to quantify the Brd4 CUT&Tag signal throughout the genome and within gene bodies
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
 
Submission date Jul 06, 2021
Last update date Sep 15, 2021
Contact name Peng zhi lin
E-mail(s) jlulin@126.com
Phone 15626213510
Organization name Sun-Yat sen university
Department zhongshan school of medicine
Lab Zhang
Street address 74 Zhongshan 2 Rd
City 广州
ZIP/Postal code 510080
Country China
 
Platform ID GPL17021
Series (2)
GSE179490 Brd4 regulates the homeostasis of CD8+ T-lymphocytes and their proliferation in response to antigen stimulation [Cut&Tag]
GSE179492 Brd4 regulates the homeostasis of CD8+ T-lymphocytes and their proliferation in response to antigen stimulation.
Relations
BioSample SAMN20066132
SRA SRX11358755

Supplementary file Size Download File type/resource
GSM5419300_BRD4_CutTag_seq_in_CD8+T_cell-2.bigwig 55.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap