|
| Status |
Public on Nov 17, 2019 |
| Title |
CTV1_PU1_delQ_6 |
| Sample type |
SRA |
| |
|
| Source name |
T cell leukemia cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CTV-1
transfected ivt mrna: PU.1_delQ
molecule subtype: transposed, nuclear DNA
|
| Treatment protocol |
Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA) and cultured for 8 hours prior to lysis procedure.
|
| Growth protocol |
CTV-1 and HEP-G2 cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum; For TALL-1 cells the culture medium was supplemented with 15% heat inactivated fetal bovine serum was used; adherent HEP-G2 cells were detached using Trypsin-EDTA (Gibco)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were treated with DNase I directly in culture medium prior to nuclear transposition procedure.
ATACseq was essentially done as described (Corces et al. 2017).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Cells were transfected with IVT mRNA and transposition was carried out 8 hours after transfection
|
| Data processing |
Raw data were aligned to the human genome (GRCh37/hg19) using bowtie2 in very-sensitive and no-discordant modes, keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). Read positions were adjusted to move the ends proximal to the Tn5 binding site (for reads on the positive strand, the start is shifted +4 bp and its partner reads start -5 bp, for reads on the negative strand, the start is shifted -5 bp and its partner reads start +4 bp) using a custom script.
Bigwigs of ChIPseq data sets were generated using HOMER v4.9 (Heinz et al, 2010) and a fixed fragment length of 65 bp. For cancer cell lines, we used the Control-FREEC v11.0 program to determine allelic imbalances from low-depth whole genome sequencing data and corrected ChIP-seq read counts accordingly to generate CNV-corrected bigWigs.
ATAC-seq peak regions were called by combining two different approaches: The basic peak region set was called using HOMER?s findPeaks program in ?region?? mode using parameters ?-size 150 -minDist 250 -L 2 -fdr 0.00001? to identify regions of variable length by stitching nucleosome-size peaks. To exclude shallow peak regions, only those were kept that overlapped a second peak set that was generated in ??factor?? mode using parameters ?-size 250 -minDist 250 -L 2 -fdr 0.00001? to identify focal peaks.
Genome_build: hg19hg19
Supplementary_files_format_and_content: coverage tracks in bigWig format (before and after CNV normalization
Supplementary_files_format_and_content: ATACseq peaks (open chromatin regions)
|
| |
|
| Submission date |
Oct 10, 2019 |
| Last update date |
Nov 18, 2019 |
| Contact name |
Michael Rehli |
| E-mail(s) |
michael.rehli@klinik.uni-r.de
|
| Organization name |
University Hospital Regensburg
|
| Department |
Internal Med III
|
| Street address |
F.-J.-Strauss-Allee 11
|
| City |
Regensburg |
| ZIP/Postal code |
93042 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE128833 |
The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [ATAC-seq] |
| GSE128837 |
The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo |
|
| Relations |
| BioSample |
SAMN13011932 |
| SRA |
SRX6975529 |
