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| Status |
Public on Aug 15, 2022 |
| Title |
A673-EWS/FLI-CUT&Tag 2 |
| Sample type |
SRA |
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| Source name |
A673 Ewing sarcoma cell line
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| Organism |
Homo sapiens |
| Characteristics |
replicate: 2
condition: parental
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| Treatment protocol |
parental cells were harvested and CUT&Tag performed using FLI1, ERG or Rabbit-IgG antiboties
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| Growth protocol |
A673 and SK-N-MC cells were cultured in DMEM with L-Glutamine, supplemented with 10% FBS, 1% PSQ, 1% sodium pyruvate at 37ºC and 5% CO2. TC-71 and TTC-466 cells were cultured in RPMI 1640 without L-Glutamine, supplemented with 10% FBS and 1% PSQ at 37ºC and 5% CO2. EWS-502 cells were cultured in RPMI 1640 without L-Glutamine, supplemented with 15% FBS and 1% PSQ at 37ºC and 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
AMPure XP bead extraction
CUT&Tag
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
A673-EWS/FLI-CUT&Tag
CUT&Tag
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| 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 EWS/FLI and EWS/ERG peak calls were generated per peak calling method described above
Supplementary_files_format_and_content: bigwig files for EWS/FLI and EWS/ERG signals compared to IgG control signals were created using deepTools
Supplementary_files_format_and_content: Overlap of EWS/FLI and EWS/ERG peaks were performed using ChIPpeakAnno, VennDiagram, GenomicRanges, and Vennerable R packages. Conserved EWS/FLI peaks were identified in A673 cells from the common overlapping peak regions within 200bps from all 5 cell lines
Supplementary_files_format_and_content: Conserved EWS/FLI peaks intersecting chromatin features like TAD boundaries, Compartment shifts and differential enhancers were identified using BEDTools
Supplementary_files_format_and_content: peaks_A673_FLI_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/FLI in A673 cells
Supplementary_files_format_and_content: peaks_TC71_FLI_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/FLI in TC71 cells
Supplementary_files_format_and_content: peaks_EWS_502_FLI_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/FLI in EWS-502 cells
Supplementary_files_format_and_content: peaks_SK_N_MC_FLI_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/FLI in SK-N-MC cells
Supplementary_files_format_and_content: peaks_TTC_466_ERG_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/ERG in TTC-466 cells
Supplementary_files_format_and_content: A673log2FLIvsIgG10.bw: bigwig tracks of EWS/FLI vs. IgG in A673 cells
Supplementary_files_format_and_content: TC71log2FLIvsIgG10.bw: bigwig tracks of EWS/FLI vs. IgG in TC71 cells
Supplementary_files_format_and_content: EWS502log2FLIvsIgG10.bw: bigwig tracks of EWS/FLI vs. IgG in EWS-502 cells
Supplementary_files_format_and_content: SKNMClog2FLIvsIgG10.bw: bigwig tracks of EWS/FLI vs. IgG in SK-N-MC cells
Supplementary_files_format_and_content: TTC466log2ERGvsIgG10.bw: bigwig tracks of EWS/ERG vs. IgG in TTC-466 cells
Supplementary_files_format_and_content: FLI_ERG_overlaps_FC4_T1_IDR0.05_FDR0.05.bed: regions overlapping EWS/FLI and EWS/ERG peak calls in A673, TC71, EWS-502, SK-N-MC, and TTC-466 cells within 200bps
Supplementary_files_format_and_content: A673_EEts_uniq.bed: EWS/FLI peaks in A673 cells underlying the regions overlapping EWS/FLI and EWS/ERG peaks in 5 cell lines
Supplementary_files_format_and_content: A673_EEts_MS_uniq.bed: Conserved EWS/FLI peaks in A673 cells at GGAA-microsatellite sites
Supplementary_files_format_and_content: A673_EEts_nonMS_uniq.bed: Conserved EWS/FLI peaks in A673 cells at non-microsatellite sites
Supplementary_files_format_and_content: homerResults_A673_EEts_uniq.html: Homer motif analysis results for conserved EWS/FLI peaks in A673 cells
Supplementary_files_format_and_content: Stable_endokd_EF_uniq.bed: Conserved EWS/FLI peaks underlying stable compartments in EF-Endo vs EF-KD
Supplementary_files_format_and_content: AB_endokd_EF_uniq.bed: Conserved EWS/FLI peaks underlying B like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: BA_endokd_EF_uniq.bed: Conserved EWS/FLI peaks underlying A like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: Stable_rskd_EF_uniq.bed: Conserved EWS/FLI peaks underlying stable compartments in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: AB_rskd_EF_uniq.bed: Conserved EWS/FLI peaks underlying B like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: BA_rskd_EF_uniq.bed: Conserved EWS/FLI peaks underlying A like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: A673EEts_EndostableEnh_uniq.bed: Conserved EWS/FLI peaks underlying stable enhancers in EF-Endo vs EF-KD
Supplementary_files_format_and_content: A673EEts_EndoGainedEnh_uniq.bed: Conserved EWS/FLI peaks underlying gained enhancers in EF-Endo vs EF-KD
Supplementary_files_format_and_content: A673EEts_EndoLostEnh_uniq.bed: Conserved EWS/FLI peaks underlying lost enhancers in EF-Endo vs EF-KD
Supplementary_files_format_and_content: A673EEts_RescuestableEnh_uniq.bed: Conserved EWS/FLI peaks underlying stable enhancers in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: A673EEts_RescueGainedEnh_uniq.bed: Conserved EWS/FLI peaks underlying gained enhancers in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: A673EEts_RescueLostEnh_uniq.bed: Conserved EWS/FLI peaks underlying lost enhancers in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: EFatstableboundaries_uniq.bed: Conserved EWS/FLI peaks underlying stable TAD boundaries between EF-Endo, EF-KD and EF-Rescue
Supplementary_files_format_and_content: EFatWTboundaries_uniq.bed: Conserved EWS/FLI peaks underlying EF-WT TAD boundaries only (boundaries that are only common to EF-Endo and EF-Rescue but not EF-KD)
Supplementary_files_format_and_content: EFatKDboundaries_uniq.bed: Conserved EWS/FLI peaks underlying EF-KD only TAD boundaries
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| Submission date |
Sep 30, 2021 |
| Last update date |
Aug 15, 2022 |
| Contact name |
Iftekhar Ahmed Showpnil |
| E-mail(s) |
[email protected]
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| Organization name |
Nationwide Children's Hospital
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| Department |
CCCBD
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| Lab |
Lessnick
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| Street address |
700 Childrens Drive
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE185126 |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (CuT&Tag I) |
| GSE185132 |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma |
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| Relations |
| BioSample |
SAMN21924302 |
| SRA |
SRX12420413 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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