 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 08, 2019 |
| Title |
Smad4KO_KC_ATAC_NoTx_382 |
| Sample type |
SRA |
| |
|
| Source name |
Smad4 flox/flox
|
| Organism |
Mus musculus |
| Characteristics |
strain: Smad4 flox/flox
treatment1: No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 50,000 cells were washed once with PBS and once with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Cells were then suspended in 50 µl 1X reaction buffer (25μl Tagment DNA Buffer, 2.5μl Tagment DNA enzyme I, and 22.5μl water) (Nextera DNA Library Preparation Kit, Illumina). Transposase reactions were carried out at 37°C for 30 minutes and immediately DNA was purified using ChIP DNA Clean & Concentrator kits (Zymo Research).
DNA was amplified using the Nextera primer Ad1 and a unique Ad2.n barcoding primer using NEBNext High-Fidelity 2XPCR Master Mix (NEB) for 14 cycles. Resulting libraries were size selected by gel excision to 175-225 bp and purified.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ATAC-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Peaks were called with HOMER for each tag directory with parameters -minDist 200 - size 200.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated HOMER peak files
|
| |
|
| Submission date |
Mar 21, 2019 |
| Last update date |
Oct 10, 2019 |
| Contact name |
Christopher K Glass |
| E-mail(s) |
ckg@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
School of Medicine
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE128659 |
Liver-derived signals sequentially reprogram myeloid enhancers to initiate and maintain Kupffer cell identity (ATAC-Seq) |
| GSE128662 |
Liver-derived signals sequentially reprogram myeloid enhancers to initiate and maintain Kupffer cell identity |
|
| Relations |
| BioSample |
SAMN11191064 |
| SRA |
SRX5551049 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3681913_Smad4KO_KC_ATAC_NoTx_382.peak.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
