|
| Status |
Public on Sep 01, 2016 |
| Title |
IFE_normal_single-end |
| Sample type |
SRA |
| |
|
| Source name |
interfollicular epidermis
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
cell type: interfollicular epidermis
gender: female
strain: mixed
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumours were dissected, minced, digested and filtered to get single cell suspension. Specific cell populations were isolated by FACS using PE-conjugated anti-CD45, PE-conjugated anti CD31, PE-conjugated anti-CD140a and APC-Cy7-conjugated anti-Epcam. Sorted cells were collected into lysis buffer for RNA extraction and ATAC-Seq.
Illumina Nextera DNA Library Prep Kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Genomic DNA of region that accessible to Tn5 transposase
ATAC-seq, protocol as described in Buenrostro et al., Nat Methods, 2013
|
| Data processing |
Library strategy: ATAC-seq
Libraries are sequenced by Illumina HiSeq 2000
Raw reads are alligned to mouse genome version mm10 though bowtie2
Peak calling were performed using HOMER on individual sequence data and pooled by mergeBed in Bedtools
Genome_build: mm10
Supplementary_files_format_and_content: The bed file with called peaks contains the union of all peaks called on individual files; text files contain read counts for genomic features. The *.count.gz file is the HTseq-count output using ATAC_peaks.bed.gz and individual bam file from sequencing alignment. The coordinates of the genomic features are contained within the file "ATAC_peaks.bed.gz".
|
| |
|
| Submission date |
Jul 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Cédric Blanpain |
| E-mail(s) |
cedric.blanpain@ulb.ac.be
|
| Organization name |
ULB
|
| Street address |
Route de Lennik 808
|
| City |
Brussels |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE70474 |
Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition [ATAC-seq] |
| GSE71621 |
Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition |
|
| Relations |
| BioSample |
SAMN03838198 |
| SRA |
SRX1079535 |
