|
| Status |
Public on Dec 01, 2023 |
| Title |
T_patch_rep3 [Sample_24157] |
| 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_24157
|
| 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 |
SAMN36660566 |
| SRA |
SRX21112402 |
