|
| Status |
Public on Dec 01, 2023 |
| Title |
LU50SCA_rep3 [Sample_15840] |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell number: 50
strain: C57BL/6J
genotype: WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh frozen lung and brain tissue sections from C57BL/6J mice were collected on a UV-activated PEN slide and further tagmented in situ using an in-house Tn5 enzyme for 1 h at 37 °C. Following, LCM was applied to collect a mini bulk of randomly captured nuclei (PALM microdissection microscope, Zeiss). Two mini-bulk sizes were investigated: 50 single-captured nuclei or 10 larger captured-areas composed each of roughly 20 nuclei, for a total of ~200 nuclei. This was applied both on brain and lung samples, at least in technical duplicates and nuclei were collected in reverse-crosslinking buffer containing Proteinase K and SDS. After reverse crosslinking at 65 °C for 1 hour, tagmented fragments were amplified, purified and sequenced paired-end on a Illumina NextSeq 2000.
Barcoded Nextera i7 and i5 primers were used to amplify the tagmented gDNA and preapare it for Illumina sequencing
ATAC-seq - Paired End 50 on a NovaSeq6000 (S1 v1.5 chemistry)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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 v3.1.3 "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 |
Nov 17, 2022 |
| 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) |
| GSE218216 |
Mouse lung and brain LCM-ATACseq |
| GSE237825 |
Mouse lung, brain and spleen LCM-ATACseq |
|
| Relations |
| BioSample |
SAMN31773301 |
| SRA |
SRX18295248 |
