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| Status |
Public on Dec 29, 2023 |
| Title |
BALBc_Ctrl_2 |
| Sample type |
SRA |
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| Source name |
peritoneal cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: macrophages
strain: BALB/c
treatment: untreated
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| Treatment protocol |
Two replicates were IL-4 treated for 4 days in BL/6 and BALB/c mice
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| Growth protocol |
Macrophage cells were isolated from the peritoneal cells by using EasySep™ Mouse F4/80 Positive Selection Kit (100-0659, Stemcell Technologies)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
100,000 macrophage cells were subjected to lysis using 100 µl of Lysis buffer (containing 10 mM Tris-Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, and 0.1% Tween-20). Following a centrifugation at 500g for 10 minutes at 4°C, the resulting nuclei were reconstituted with 50 µl of a transposition mixture (FC-121-1030, Illumina; comprising 1X Tagment DNA buffer, Tn5 Transposase, and nuclease-free H2O), and this mixture was then incubated for 30 minutes at 37°C in a thermomixer. The transposed DNA was subsequently purified using MinElute columns (28004, QIAGEN) and then amplified using Nextera sequencing primers and the NEB high-fidelity 2X PCR master mix for 11 cycles (M0541, New England Biolabs). PCR-amplified DNA was purified using MinElute columns
ATAC-seq samples were pooled and sequenced on NextSeq 2000 P2 using PI lab prepared library and paired-end sequencing.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
TheReal Time Analysis software (RTA 3.9.25) was used for processing raw data files, the Illumina bcl2fastq v2.17 was used to demultiplex and convert binary base calls and qualities to fastq format.
Samples were trimmed for adapters using Cutadapt (1.18) before the alignment.
The trimmed reads were aligned with mm10 reference using Bowtie2(2.2.6) alignment.
The peaks were called using Genrich (0.6.1) (genrich -t sample_sortedByRead.bam -o sample.narroPeak -j -y -r -v -d 150 -m 5 -e chrM,chrY -E blacklist_regions.bed-f sample.bdg -b sample.bed)
Assembly: mm10
Supplementary files format and content: bigwig files were generated using Genrich (0.6.1)
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| Submission date |
Nov 16, 2023 |
| Last update date |
Dec 29, 2023 |
| Contact name |
Mingming Zhao |
| E-mail(s) |
mingming.zhao@nih.gov
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| Organization name |
national institutes of health
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| Street address |
9000 Rockville Pike
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| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL30172 |
| Series (2) |
| GSE248022 |
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [ATAC-seq] |
| GSE248038 |
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS |
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| Relations |
| BioSample |
SAMN38286061 |
| SRA |
SRX22550716 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7904806_BALBc_Ctrl_2.genrich.RPM.bw |
389.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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