|
| Status |
Public on Dec 12, 2016 |
| Title |
mTEC Lo ATAC-Seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
Immature mTECs from WT mice
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Thymic EpCAM+Ly51-MHCIIlo
strain: C57BL/6
age: 6 weeks-old
|
| Growth protocol |
Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrifised at 6weeks of age by CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were FACS sorted into MACS buffer and the open chromatin was profiled by the ATAC-seq protocol developed by (Buenrostro et al., 2013) with modifications described by (Lara-Astiaso et al., 2014).
protocol developed by (Buenrostro et al., 2013).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
fastq using bcl2fastq
alignment using bowtie2 (--local, mm9)
filter out reads that align to same place and sequence on R2 from nucleotides #1 to #15 are identical
makeTagDirectory -tbp
makeUCSCfile -bigWig -fsize 1e20
Genome_build: mm9
|
| |
|
| Submission date |
Nov 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jakub Abramson |
| E-mail(s) |
jakub.abramson@weizmann.ac.il
|
| Organization name |
Weizmann Institute
|
| Department |
Immunology
|
| Street address |
Herzl 234
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE90048 |
Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells [ATAC-Seq] |
| GSE90050 |
Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells |
|
| Relations |
| BioSample |
SAMN06039811 |
| SRA |
SRX2359710 |
