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Sample GSM7226976

Query DataSets for GSM7226976

Status

Public on Jan 26, 2024

Title

WGSPF1:Negativecontrol,1stpenning c

Sample type

SRA

Source name

Blood

Organism

Mus musculus

Characteristics

tissue: Blood
cell line: P388D1 derived PF3
cell type: monocyte, macrophage
genotype: stable FastFUCCI expression
treatment: None

Treatment protocol

PF1 cells were treated with 5,000 microjoules/cm2 of UVC and penned as single cells directly after treatment. Negative control cell samples were taken from the proliferating population at the time of treatment.

Growth protocol

The PF1 line (P388D1 with FastFUCCI integration) was maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

Extracted molecule

genomic DNA

Extraction protocol

For PF1 cells, DNA extraction was performed using the DNeasy kit from Qiagen© as per the manufacturer's instructions. For the F1 mouse tumours, DNA was extracted using the Qiagen© AllPrep DNA/RNA Mini Kit.
Approximately 100-500 µg of genomic DNA was fragmented and libraries prepared using the NEBNext® Ultra II kit and the Unique Dual Index primers for Illumina® as per the manufacturer’s instructions, with the exception that the enzymatic fragmentation step was carried out for 15 minutes instead of 5.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Description

PF1_Neg1c
PF1_SisterMutations.rds

Data processing

PF1 whole genome-sequencing: Reads were trimmed using trim-galore and mapped with Bowtie2 to the mm10 reference. Mutations were called using Manta and Strelka2, filtered with bamtools and the GATK tool CalculateSNVMetrics
F1 tumour whole genome-sequencing: Reads were trimmed using trim-galore and mapped with Bowtie2 to an N-masked mm10 reference created with SNPsplit. Reads were then haplotype labeled using snpsplit. Mutations were called using Manta and Strelka2, filtered with bamtools and the GATK tool CalculateSNVMetrics. Haplotype identification was done by counting assignable reads (minimum of 2) for each mutation, and fitting a dual gaussian distribution with mixtools
Omni-ATAC: Reads were mapped with Bowtie2 and peaks called with MACS2 using the flags -f BAMPE -g mm –nomodel –nolambda –keep-dup-all –call-summits -B -q 0.01. The peak file here is from sample 1 which was used in all comparisons.
RNA-seq: Transcript abundances were quantified using Kalisto (v0.46.0) with the –bias and –rf-stranded flags and the Gencode M25 transcript release. Transcription start sites were adjusted to the isoform with the highest ATAC signal within -1000 - +500 from the promoter
Assembly: mm10
Supplementary files format and content: PF1_SisterMutations.rds: RDS file of mutations in all 14 PF1 genomes (7 pairs of sisters). Contains chromosome, position, reference base, alternate base, QC metrics from CalculateCNVMetrics (Info), counts for each base type, coverage, filter, timepoint (T0=penning, T1=post penning) and sample name
Supplementary files format and content: PF1_RNA_counts.rds: Tags per million (tpm) ouput from Kallisto for 3 replicates. Entrez gene ID, gene name and genomic positions are noted.
Supplementary files format and content: PF1_ATAC_Peaks.rds: ATAC peak file in RDS format from MACS2 peak calling
Supplementary files format and content: F1CastB6_mutations.rds: RDS file of mutations in all 6 F1 tumors. Contains chromosome, position, reference base, alternate base, QC metrics from CalculateCNVMetrics (Info), counts for each base type, coverage, filter and sample name
Library strategy: WGS

Submission date

Apr 25, 2023

Last update date

Jan 26, 2024

Contact name

Paul Adrian Ginno

E-mail(s)

p.ginno@dkfz-heidelberg.de

Phone

00496221423395

Organization name

DKFZ