|
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
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|
|
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 |