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| Status |
Public on Mar 31, 2018 |
| Title |
WT_rabbit IgG_ChIP-Seq |
| Sample type |
SRA |
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| Source name |
leukemic bone marrow cells
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| Organism |
Mus musculus |
| Characteristics |
strain: Gfi1b(fl/fl) x Nup98(tg) x MxCre(wt)
tissue: bone marrow
cell type: leukemic bone marrow cells
chip-antibody: rabbit-IgG, Sigma, I5006
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bone marrow (BM) cells were isolated from Gfi1bfl/fl MxCretg NUP98/HOXD13tg and Gfi1bfl/fl MxCrewt Nup98/HOXD13 mice. BM cells were homogenised and ery lysis was performed. 1x10^7 cells were fixed with 1% formaldehyde and sonicated for 20 min. Histone-DNA antibody were isolated with antibody
Libraries were prepared using the NEBNext® UltraTM DNA Library Prep Kit for Illumina®. Samples were pooled after quality check.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
CK32_GATCAG_L001_R1_001.fastq.gz
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| Data processing |
Basecalls were performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using the Unipro-UGENE software using the BWA-MEM algorithm. Workflow: Filtration of the Input sequencing reads by the CASAVA header, cutting of adaptersequences, trimming of the sequencing reads by quality, mapping of the reads to reference sequence mouse MM10 (GRCm38), filtratoin of aligned reads by SAM-tools to remove reads with low mapping quality, unaligned / unpaired reads etc, removal of PCR duplicates, conversion to BAM format. The workflow also performs quality control of the data with FastQC: first on the input FASTQ files, second after the preprocessing step.
BAM-file indexes were generated using samtools
BAM files were analyzed using SeqMonk V 0.32.1 and peak-probes were defined using the MACS algorithm using Chip-Seq samples CK31.bam,CK34.bam and IgG control samples CK32.bam,CK35.bam. Fragment size was 300. Significance threshold was 1.0E-5.. Quantitated with Read Count Quantitation using All Reads correcting for total count only in probes per million reads log transformed. Quantitation output was generated by SeqMonk as "feature report" quantitating probes overlapping annotated genes.
Subsequently, H3K9ac probe-levels were analyzed by ALtAnalyze V2.0 (default parameters but: data type: Other ID; platform: Ensembl; process expression file; species: Mm, filter_method: z-score, z_threshold: 1.96, p_val_threshold: 0.05, change_threshold: 2, sort_only_by_zscore: yes, analysis_method: non-UI, enrichment_type: ORA, ORA Parameters: mod: Ensembl, permutations: FisherExactTest, resources_to_analyze: all
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table of normalized abundance measurements as tab delimited txt-file with gene level probe quantitations and additional information: Chr, Start, End, Feature ID, Description, No. Sublocations, No. Probes, Mean CK31.bam, StDev CK31.bam, Mean CK34.bam, StDev CK34.bam
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| Submission date |
Oct 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cyrus Khandanpour |
| E-mail(s) |
cyrus.khandanpour@uk-essen.de
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| Organization name |
University Hospital Of Essen
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| Department |
Department of Hematology
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| Lab |
WTZ-Forschungsgebäude 2.OG
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| Street address |
Hufelandstr. 55
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| City |
Essen |
| State/province |
NRW |
| ZIP/Postal code |
45147 |
| Country |
Germany |
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| Platform ID |
GPL9185 |
| Series (2) |
| GSE88934 |
Gfi1b - A key player in genesis and maintenance of AML and MDS [ChIP-seq] |
| GSE88935 |
Gfi1b - A key player in genesis and maintenance of AML and MDS |
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| Relations |
| BioSample |
SAMN05924462 |
| SRA |
SRX2252015 |
| 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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