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| Status |
Public on Nov 06, 2019 |
| Title |
H3K4me2_KDR1_ChIPSeq |
| Sample type |
SRA |
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| Source name |
SW480 Cells
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| Organism |
Homo sapiens |
| Characteristics |
genotype: LSD1 knockdown
chip antibody: H3K4me2 (Millipore, 17-677, lot 2420415)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were trypsonized prior to histone ChIP-seq (iDeal ChIP-seq Kit for Histones, Diagenode: C01010051) or scraped prior to transcription factor ChIP-seq (iDeal ChIP-seq kit for Transcription Factors, Diagenode: C01010055).
Libraries were generated for sequencing using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) per manufacturer’s protocol.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
LSD1 knockdown replicate 1
K4me2-merge_KD_intersect.bed
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| Data processing |
Quality of sequencing reads assessed with FastQC (v0.11.5).
Reads were aligned to the hg38 genome using Bowtie2 (v2.3.2) with additional parameters -q --phred33 --sensitive --end-to-end --no-unal --no-mixed --no-discordant. The Bowtie2 genome index used for alignment was downloaded from Illumina iGenomes on Sun Jan 27 02:01:22 EST 2019.
SAM files were coordinate sorted and indexed using Samtools (v1.9).
Peaks were called using MACS (v2.1.0) with the appropriate input or KO controls, with additional parameters -g hs -q 0.05
Bedtools (v2.26.0) was used to find intersecting peaks between replicates.
bigWigs were created using deepTools (v3.1.3) bamCoverage with additional parameters -bs 1 --normalizeUsing CPM and --extendReads 150 for single end, or --extendReads for paired end samples.
Genome_build: hg38
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: bigwig
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| Submission date |
Nov 05, 2019 |
| Last update date |
Nov 07, 2019 |
| Contact name |
Robert Policastro |
| Organization name |
Ensoma Inc.
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| Street address |
451 D St Unit #600
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02210 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE139925 |
LSD1 mediates AKT activity in PIK3CA mutant colorectal cancer [ChIP-Seq] |
| GSE139927 |
LSD1 mediates AKT activity in PIK3CA mutant colorectal cancer |
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| Relations |
| BioSample |
SAMN13197718 |
| SRA |
SRX7100366 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4149686_SW480_LSD1_KD_H3k4me2_ChIP_1.bigwig |
405.9 Mb |
(ftp)(http) |
BIGWIG |
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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