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| Status |
Public on Feb 06, 2020 |
| Title |
ATAC7 |
| Sample type |
SRA |
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| Source name |
colon epithel
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| Organism |
Mus musculus |
| Characteristics |
treatment: No treatment
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh crypts were extracted and dissociated into single cells. 50,000 cells were sorted and pelleted by centrifugation for 5 min at 500 g and 4°C. Cell pellets were washed once with 1xPBS and pelleted again. Cell pellets were resuspended in 25 µl of lysis buffer and nuclei were pelleted. Supernatant was discarded and nuclei were re-suspended in 50 µl reaction buffer containing 2.5 µl of Tn5 transposase and 25 µl of TD buffer.
Sequencing libraries were prepared using DNA purification (QIAquick minelute columns, Qiagen) and amplification by PCR using Nextera complimentary primers. Paired-end sequencing was performed on an Illumina HiSeq 2000 machine by multiplexing three samples on one lane.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina RTA 1.18.64 software used for basecalling.
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Read mapping: Bowtie2
Peak calling: MACS2
Calling of count data: htseq.py
Genome_build: mm9
Supplementary_files_format_and_content: Individual peaks, total merged peaks and count tables for all samples
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| Submission date |
Dec 04, 2019 |
| Last update date |
Jun 17, 2020 |
| Contact name |
Guenter Raddatz |
| Organization name |
German Center for Cancer Research
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| Street address |
Im Neuenheimer Feld 580
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE137037 |
The intestinal microbiota programs DNA methylation to control tissue homeostasis and inflammation |
| GSE141458 |
The intestinal microbiota programs DNA methylation to control tissue homeostasis and inflammation [ATAC-Seq] |
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| Relations |
| BioSample |
SAMN13480929 |
| SRA |
SRX7267721 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4203633_ATAC7.peaks.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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