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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 25, 2020 |
| Title |
Exp1_45min |
| Sample type |
SRA |
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| Source name |
HAP1
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| Organism |
Homo sapiens |
| Characteristics |
Sex: male
tissue: bone marrow
disease: Chronic Myeloid Leukemia
digestion time: 45 min
growth protocol: IMDM + 10% FBS
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| Treatment protocol |
In situ HindIII/MboI digestion, dephosphorylation, linker ligation
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| Growth protocol |
IMDM + 10% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Phenol-chlorophorm DNA extraction
DNA shearing, In Vitro Transcription, RNA clean-up, RA3(Illumina)-adapter ligation, Reverse Transcription, PCR, DNA clean-up
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
BED file generated by gpseq-seq-gg (v2.0.2/3) pipeline. Briefly performs: pattern filtering with scan_for_matches, mapping with bwa-mem (v0.7.17), mapping filtering, detection of orphan reads, quality filtering, UMI de-duplication.
BED files are corrected for chromosome translocations using bed-fix-chrom-rearrangement (v0.0.1, d.o.i.: 10.5281/zenodo.3365906).
GPSeq score is estimated from the translocation-corrected BED files using the gpseqc (v2.3.6) pipeline.
chromflock (v0.1) was used to build 3D genome structures.
Genome_build: Grch37/hg19
Supplementary_files_format_and_content:
bed; UCSC BED format with chromosome, chromStart, chromEND, name, and de-duplicated UMI count per cutsite. Generated by the gpseq-seq-gg pipeline.
transCorrected.bed; UCSC BED format corrected for chromosome translocations.
zipped gpseqc output; see supplementary files format below.
settings.txt; settings for gpseqc pipeline
log.txt; log of gpseqc pipeline run
combined.tsv; gpseqc pipeline intermediate table
estimated.tsv; raw GPSeq score estimated by gpseqc pipeline
rescaled.tsv; rescaled GPSeq score estimated by gpseqc pipeline
zipped chromflock output; see chromflock.README.md
csv (chromflock bead labels)
markdown
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| Submission date |
Aug 19, 2019 |
| Last update date |
May 26, 2020 |
| Contact name |
Gabriele Girelli |
| E-mail(s) |
[email protected]
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| Organization name |
Karolinska Institutet / Science for Life Laboratory
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| Department |
MBB
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| Lab |
Bienko lab
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| Street address |
Tomtebodavägen 23A
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| City |
Solna |
| State/province |
Stockholm |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE135882 |
GPSeq Reveals the radial organization of chromatin in the cell nucleus |
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| Relations |
| BioSample |
SAMN12603158 |
| SRA |
SRX6742747 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4039374_Exp1_45min.bed.gz |
6.8 Mb |
(ftp)(http) |
BED |
| GSM4039374_Exp1_45min.transCorrected.bed.gz |
6.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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