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| Status |
Public on Jun 18, 2022 |
| Title |
K562 CUT&Tag IgG control Replicate B |
| Sample type |
SRA |
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| Source name |
K562
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
chip antibody: anti-IgG antibody (Cell signaling, Normal Rabbit IgG #2729)
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| Growth protocol |
K562 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1X penicillin streptomycin antibiotic.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
24h prior to the experiment, cells were split at a final concentration of 0.5 million cells/mL in fresh RPMI + 10% FBS + Antibiotic-antimycotic. PARP1 CUT&Tag was done in two replicates with 250,000 K562 cells each for baseline control and anti-PARP1 CUT&Tag. Experiments were done according to the bench top CUT&Tag V.3 protocol developed by the Henikoff lab (Kaya-Okur et al. protocols.io, 2020). using CUTANA™ Concanavalin A Conjugated Paramagnetic Beads (EpiCypher, SKU: 21-1401) and pAG-Tn5 for CUT&Tag (EpiCypher, SKU: 15-1017), with the following exceptions: (A) cells were not cross-linked and (B) NE1 buffer was used to extract and permeabilize nuclei. For anti-PARP1 CUT&Tag, we used an antibody against the N-terminal of PARP1 (Active Motif, AB_2793257). An anti-IgG antibody (Cell signaling, Normal Rabbit IgG #2729) was used as baseline control.
Library construction protocol was as described at the bench top CUT&Tag V.3 protocol developed by the Henikoff lab (Kaya-Okur et al. protocols.io, 2020).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CUT&Tag
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| Data processing |
fastq files were trimmed from Nextera adaptor-associated sequences using cutadapt
trimmed fastq files were mapped to hg38 human genome assembly using bowtie2
We then used bedtools genomecov to generate bedgraph files and calculated background-normalized PARP1 binding using macs2 bdgcmp command
Supplementary files format and content: bigwig files - containing either raw counts or baseline-normalized fold-enrichment scores
Library strategy: CUT&Tag
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| Submission date |
Jun 13, 2022 |
| Last update date |
Jun 18, 2022 |
| Contact name |
Charles Grahe Danko |
| E-mail(s) |
dankoc@gmail.com
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| Organization name |
Cornell University
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| Department |
Baker Institute for Animal Health
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| Street address |
235 Hungerford Hill Road
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE206022 |
RNA polymerase II and PARP1 shape enhancer-promoter contacts [CUT&Tag] |
| GSE206133 |
RNA polymerase II and PARP1 shape enhancer-promoter contacts |
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| Relations |
| BioSample |
SAMN29012064 |
| SRA |
SRX15688503 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6238994_K562_IgG_CUTnTag_B_raw.bw |
17.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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