|
| Status |
Public on Aug 15, 2022 |
| Title |
TC71-EFEndo-CTCF-CUT&Tag 1 |
| Sample type |
SRA |
| |
|
| Source name |
TC71 Ewing sarcoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
replicate: 1
transduced shrna: iLuc
condition: EF-Endo
|
| Treatment protocol |
EWS/FLI knock-down with RNAi followed by rescue of EWS/FLI expression with a 3XFLAG tagged EWS/FLI cDNA construct
|
| Growth protocol |
A673 cells were cultured in DMEM with L-Glutamine, supplemented with 10% FBS, 1% PSQ, 1% sodium pyruvate for 2-3 days, followed by selection in the same media supplemented with 2μg/mL puromycin, and 150μg/mL hygromycin B at 37ºC and 5% CO2. TC71 cells were cultured in RPMI 1640 without L-Glutamine, supplemented with 10% FBS and 1% PSQ at 37ºC and 5% CO2 for 2 days, followed by selection in the same media supplemented with 2μg/mL puromycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AMPure XP bead extraction
Cleavage Under Target & Tagmentation (CUT&Tag)
CUT&Tag
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
TC71-EFEndo-CTCF-CUT&Tag
CTCF CUT&Tag
|
| Data processing |
Adapter sequences and low quality reads were trimmed using Trim Galore
Reads aligned to human hg19 and E.Coli genomes using Bowtie2
Reads were spike-in normalized using DESeq2 median ratio method
Peaks were called with spike-in normalization using corresponding IgG as controls, and accounting for variation between the biological replicates using MACS2 (v 2.2.7.1; Zhang et al., 2008), DiffBind (v2.14.0; Ross-Innes et al., 2012; Stark R., 2011) and DESeq2
Spike-in normalized bigwig tracks were generated and averaged across biological replicates using deepTools
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files containing CTCF peak calls were generated per peak calling method described above
Supplementary_files_format_and_content: bigwig files for CTCF signals compared to IgG control signals were created using deepTools
Supplementary_files_format_and_content: Overlap of CTCF and TAD boundaries were performed using BEDTools
Supplementary_files_format_and_content: CTCF localization matrix at stable, EF-WT and EF-KD TAD boundaries was generated using deepTools
|
| |
|
| Submission date |
Sep 30, 2021 |
| Last update date |
Aug 15, 2022 |
| Contact name |
Iftekhar Ahmed Showpnil |
| E-mail(s) |
[email protected]
|
| Organization name |
Nationwide Children's Hospital
|
| Department |
CCCBD
|
| Lab |
Lessnick
|
| Street address |
700 Childrens Drive
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE185127 |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (CUT&Tag II) |
| GSE185132 |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma |
|
| Relations |
| BioSample |
SAMN21924356 |
| SRA |
SRX12421594 |
