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| Status |
Public on Apr 30, 2019 |
| Title |
ATAC-seq_HAP1_BCL11A_r1_2426_10 |
| Sample type |
SRA |
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| Source name |
HAP1 cell line
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| Organism |
Homo sapiens |
| Characteristics |
library: ATAC-seq
cell line: HAP1
replicate: 1
clone: 10-2426
knockout: BCL11A
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| Growth protocol |
HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50000 cells were resuspended in 25 µl transposase reaction mix (0.05% digitonin, 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
ATAC-seq on HAP1 cell line with BCL11A knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv
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| Data processing |
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: Each csv file contains read counts for each sample for each regulatory element
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| Submission date |
Dec 21, 2017 |
| Last update date |
May 07, 2019 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
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| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
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| Street address |
Lazarettgasse 14
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE108386 |
Systematic functional characterization of BAF mutations yields novel intra-complex synthetic lethalities [ATAC-Seq] |
| GSE108390 |
Systematic functional characterization of BAF mutations yields novel intra-complex synthetic lethalities |
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| Relations |
| BioSample |
SAMN08224397 |
| SRA |
SRX3503114 |
| 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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