|
| Status |
Public on Oct 03, 2019 |
| Title |
dipg33.1,dipg33.2 End-repair and A-tailing |
| Sample type |
SRA |
| |
|
| Source name |
patient-derived cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: H3K27Ac (Active Motif #39133)
|
| Growth protocol |
TSM base + EGF/FGF/PDGF-AA/PDGF-BB, see Grasso 2015
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells are fixed with 1% FA. Following ChIP and washes, DNA is purified using PCI purification
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
dipg33.1,dipg33.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG33 patient-derived DIPG culture
cell culture ChIP-seq
|
| Data processing |
ChIP-seq reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Peaks were called using macs2 version 2.1.1.20160309 callpeak on full depth bam files over input controls. Broad peak calling was used for H3K27me3 and EED
Genome_build: hg19
Supplementary_files_format_and_content: RPM bigwig
ChIP-Rx reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference and then unmapped reads (--un-conc) were aligned to dm6 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates from both hg19 and dm6 alignments
Normalization to 1M dm6 reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: RRPM bigwig
RNA-seq reads were trimmed of adaptors with cutadapt
Aligned to hg19 with tophat2 v2.1.1
Reads counted in hg19 RefSeq genes using featureCounts
Transcript per million (TPM) for each gene was determined as 1,000,000 * (reads per kilobase of transcript)/(total sum of reads per kilobase of all transcripts)
Genome_build: hg19
Supplementary_files_format_and_content: TPM spreadsheet
ATAC-seq reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Full depth technical replicate bam files were then merged with samtools merge and peak calls we performed once more on the merged replicate file using macs2 version 2.1.1.20160309
Genome_build: hg19
Supplementary_files_format_and_content: RPM bigwig
WES/WGS reads were trimmed of adaptors with cutadapt
Reads were aligned to the hg19 reference sequence using bwa mem v0.7.15. PCR duplicates were removed using picardtools MarkDuplicates.
Reads were then processed using GATK best practices, including indel realignment and base recalibration
Variants were called with GATK UnifiedGenotyper
Genome_build: hg19
Supplementary_files_format_and_content: VCF variant calls
|
| |
|
| Submission date |
Feb 08, 2019 |
| Last update date |
Oct 05, 2019 |
| Contact name |
Michelle Monje |
| E-mail(s) |
mmonje@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
265 Campus Drive, SIM1 G3035
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE126319 |
Variant and cell-context specific H3K27M reprogramming results in distinct enhancer architecture and oncogenic states |
|
| Relations |
| BioSample |
SAMN10904558 |
| SRA |
SRX5353195 |
