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| Status |
Public on Mar 06, 2018 |
| Title |
RELACS HepG2 input |
| Sample type |
SRA |
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| Source name |
HepG2
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| Organism |
Homo sapiens |
| Characteristics |
cell type: liver hepatocellular carcinoma
provider/strain: ATCC, HB-8065
chip antibody: none
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| Growth protocol |
HepG2 (ATCC, HB-8065TM) were culture in EMEM (Lonza, 06-174) supplemented with 10% FBS, 2 mM L-Glutamine, 1.8 mM CaCl2, 1mM sodium pyruvate and penicillin-streptomycin mixture (100 units/ml, Lonza), at 37 ˚C at 5% CO2. S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27°C. Mouse experiments were performed on 9 weeks-old wild-type (WT) FVB/NJ littermate male mice fed chow diet and maintained on a 12h light cycle (lights on at 7 am).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
RELACS: nuclei have been extracted, permeabilized and barcoded following RELACS protocol. Nuclei labeled with distinct barcodes have been pooled and lysed to complete chromatin preparation. Traditional ChIP-seq: after nuclei extraction chromatin has been fragmented by sonication. Immunoprecipitation has been performed using the antibody of interest.
RELACS libraries: as described in the paper, using A-tailing strategy and ligation of adapters containing nuclear barcodes. After ChIP and DNA purification library preparation has been completed by PCR amplification using NEB workflow (NEBNext Ultra II DNA library preparation kit (E7645L, NEB)). Traditional ChIP-seq libraries: NEBNext Ultra II DNA library preparation kit (E7645L, NEB)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
each ChIP contains 20 technical replicates identified by different RELACS barcodes. Chromatin amount per input: 1% of ChIP volume
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| Data processing |
ChIP-seq reads were aligned to the mm10 and hs37d5 genome assembly using Bowtie2-2.2.8 with the following configuration: -X 1000 --local --fr --rg CN:mpi-ie_deep_sequencing_unit --rg PL:ILLUMINA
Data were sorted and indexed using samtools-1.3.1, then filtered with deeptools3 in all downstrean analysis using the following specifications: --ignoreDuplicates --blackListFileName
Reads different quality measurments were assesed using FastaQC/0.11.3, fastq_screen/0.5.1, and MultiQC/1.3
Chips were explored using different tools within deeptools3: bamCoverage, bamCompare, multiBigwigSummary, plotCorrelation, computeMatrix, plotEnrichment, plotProfile, plotFingerprint, plotHeatmap
Peaks were called using MACS2-2.1.0 callpeak with the following configurations: -f BAM -g 2900338458 --keep-dup all --nomodel; and using histoneHMM/histone_call_regions.R -b 750 -P 0.1
Genome_build: mouse: mm10, human: hs37d5
Supplementary_files_format_and_content: txt,bed,gff,bigwig
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| Submission date |
Feb 22, 2018 |
| Last update date |
Sep 07, 2018 |
| Contact name |
Thomas Manke |
| E-mail(s) |
manke@ie-freiburg.mpg.de
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| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Street address |
Stuebeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE111000 |
Ultra-parallel ChIP-seq by barcoding of intact nuclei |
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| Relations |
| BioSample |
SAMN08580677 |
| SRA |
SRX3733789 |
| 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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