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Sample GSM7111677 Query DataSets for GSM7111677
Status Public on Jun 01, 2023
Title Lin_neg_9mo_Tet2_WT
Sample type SRA
 
Source name Lin_neg
Organism Mus musculus
Characteristics cell type: Lin_neg
strain: Mixed 129/C57BL/6
genotype: Tet2_WT
age: 9mo
Growth protocol Bone marrow was harvested and LSK (Lin-, Sca1+, cKit+) and Lin– (lineage negative) cells sorted by FACS.
Extracted molecule total RNA
Extraction protocol For RNA-seq, RNA extraction was performed using Qaigen RNeasy Total RNA kit. For WGBS, DNA extraction was performed using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description M16LN9W
Data processing For RNA-seq RNA was extracted using Qaigen RNeasy Total RNA kit I. Library preparation and mRNA sequencing were performed at Novogene using their Illumina Novoseq 6000 platform. Adaptors were trimmed using trim galore (v0.6.5) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.3a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with edgeR (FDR <0.05 and fold-change >1.0), following the standard package documentation.
For WGBS, DNA was extracted by Quick-DNA miniprep kit (Zymo, D3024) following the manufacturer’s instructions. Bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.4% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (v1.5.5) (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.22.3) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor.
Assembly: mm10
 
Submission date Mar 22, 2023
Last update date Jun 01, 2023
Contact name Meelad M Dawlaty
E-mail(s) meelad.dawlaty@einsteinmed.org
Phone 718-678-1224
Organization name Albert Einstein College of Medicine
Department Genetics
Lab Dawlaty Lab
Street address 1301 Morris Park Ave, Price 419, Bronx
City New York
State/province New York
ZIP/Postal code 10461
Country USA
 
Platform ID GPL24247
Series (1)
GSE227977 Comparative analysis of Tet2 catalytic deficient and knockout bone marrow over time
Relations
BioSample SAMN33864144
SRA SRX19750514

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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