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Sample GSM7655015 Query DataSets for GSM7655015
Status Public on Dec 01, 2023
Title T_patch_rep1 [Sample_24154]
Sample type SRA
 
Source name spleen
Organism Mus musculus
Characteristics tissue: spleen
cell number: 1000
cell type: Tcell
genotype: wt
strain: C57BL/6J WT
Extracted molecule genomic DNA
Extraction protocol ATAC-seq - Paired End 50 on a NovaSeq6000 (SP v1.5 chemistry)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Sample_24154
Data processing Demultiplexing was perfomed using bcl2fastq2 v2.20
Adapter trimming was performed using Trimmomatic v0.36 with following parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36 CROP:48
Alignment was performed using bowtie2 v2.4.5 against the human reference genome mm10.
Duplicated reads were removed using picard "dedup" function and the transposase-induced offset was removed using the deeptools v3.5.2 "alignmentSieve" function.
Sorting and indexing of bam files was done using samtools v1.14
Peak calling was performed using MACS2 v2.2.7.1. on sample merged .bam file
Quantification of sequencing reads in unified peak regions was performed in R 4.1.0 using the "summarizeOverlaps" function implemented in the GenomicAlignments package v1.28.0.
Assembly: mm10
Supplementary files format and content: comma separated files include raw count table
 
Submission date Jul 20, 2023
Last update date Dec 01, 2023
Contact name Joachim Schultze
E-mail(s) j.schultze@uni-bonn.de
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
 
Platform ID GPL24247
Series (2)
GSE237824 Mouse spleen LCM-ATACseq (B and T cell zones)
GSE237825 Mouse lung, brain and spleen LCM-ATACseq
Relations
BioSample SAMN36660569
SRA SRX21112399

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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