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Sample GSM7711978 Query DataSets for GSM7711978
Status Public on Feb 29, 2024
Title 2 wk HSC biol rep 3
Sample type SRA
Source name bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
age: 2 weeks
Sex: pooled male and female
cell type: LinnegcKitposSca1posFlk2negCD150posCD48neg
genotype: C57Bl/6 wild-type
treatment: steady state isolation
Extracted molecule polyA RNA
Extraction protocol RNA was isolated from 5000 - 20,000 HSPCs using the RNeasy Plus Micro Kit (Qiagen, 74034). RNA integrity number (RIN) was determined by Bioanalyzer (Agilent Technologies) and RNA samples with RIN > 9.0 were further processed. RNA samples were processed over multiple experimental “sort days” and stored at -80°C in RNA isolation buffer until library preparation. A total of 3biological replicates were sequenced for each population. RNA was quantified and QC using an Agilent Bioanalyzer. Illumina sequencing libraries were prepared and sequenced at the NYU Genome Technology Center (New York, NY).
The NuGen Ovation Trio low input RNA-seq library preparation kit was used for library preparation.
All libraries were prepared at the same time in order to minimize batch effects. Libraries were sequenced using an Illumina NovaSEQ 6000 instrument with paired end 50 base pair sequencing to a target depth of 40 million unique reads per sample.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Sequencing QC was performed using FastQC and MultiQC.
Paired-end reads were mapped to the mouse reference genome (GRCm38 ver104) using STAR and quantified with Feature Counts
Assembly: GRCm38 ver104
Supplementary files format and content: tab-delimited text files contain raw counts for each sample
Submission date Aug 15, 2023
Last update date Feb 29, 2024
Contact name Melissa Proven
Organization name Columbia Unversity
Lab Passegue
Street address 650 W 168 ST
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platform ID GPL24247
Series (2)
GSE240912 Maternal IL-10 restricts fetal emergency myelopoiesis [Bulk RNA-seq]
GSE240915 Maternal IL-10 restricts fetal emergency myelopoiesis
BioSample SAMN36996117
SRA SRX21375308

Supplementary file Size Download File type/resource
GSM7711978_2wk_HSC_4.counts.unstr.txt.gz 179.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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