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| Status |
Public on Sep 08, 2018 |
| Title |
RELACS Input (4 replicates), 4 base UMI |
| 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: CTCF (Abcam, ab70303)
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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 3000 |
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| Description |
5 biological replicates of HepG2 cells with the indicated UMI strategy.
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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
BigWig files were created with bamCoverage (deepTools 2.4.1) using `-e --normalizeTo1x -bs 50`
Genome_build: mouse: mm10, human: hs37d5
Supplementary_files_format_and_content: BigWig files contain coverage information generated from genomic alignments.
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| Submission date |
Sep 07, 2018 |
| Last update date |
Sep 10, 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 |
GPL21290 |
| Series (1) |
| GSE111000 |
Ultra-parallel ChIP-seq by barcoding of intact nuclei |
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| Relations |
| BioSample |
SAMN09990360 |
| SRA |
SRX4655788 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3380029_RELACS_Input_4ntUMI_bar_16.seq_depth_norm.bw |
19.0 Mb |
(ftp)(http) |
BW |
| GSM3380029_RELACS_Input_4ntUMI_bar_18.seq_depth_norm.bw |
21.0 Mb |
(ftp)(http) |
BW |
| GSM3380029_RELACS_Input_4ntUMI_bar_2.seq_depth_norm.bw |
18.5 Mb |
(ftp)(http) |
BW |
| GSM3380029_RELACS_Input_4ntUMI_bar_20.seq_depth_norm.bw |
21.1 Mb |
(ftp)(http) |
BW |
| GSM3380029_RELACS_Input_4ntUMI_bar_5.seq_depth_norm.bw |
15.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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