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Sample GSM2850386 Query DataSets for GSM2850386
Status Public on Mar 06, 2018
Title FL iLS_8h after treatment rep3
Sample type SRA
Source name FL iLS_8h after treatment
Organism Mus musculus
Characteristics strain: C57BL/6J
cell type: fetal liver induced leukocyte stem cell (FL iLS)
time point: 8h after treatment
Treatment protocol To induce B cell differentiation of iLS cells, the cells were co-cultured with TSt-4 cells in IMDM medium supplemented with 5 ng/ml IL-7 in the absence of 4-OHT.
Growth protocol Id3-ERT2-induced hematopoietic multipotent progenitors (induced leukocyte stem, or iLS cells) were co-cultured with TSt-4 feeder cells in IMDM medium supplemented with 20 ng/mL IL-7, 10 ng/mL SCF, 10 ng/mL Flt-3L and 40 nM 4-OHT.
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using Maxwell 16LEV simplyRNA purification kit.
Poly(A)+ mRNA was isolated from total RNA by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) then library was prepared by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Average size and quantity of each library were measured by Agilent 2100 Bioanalyzer (Agilent Technologies) and KAPA Library Quantification Kit (KAPA Biosystems), respectively. Sequences were read by HiSeq 1500 system (Illumina).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description S02472
Data processing Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned on mouse genome (mm9) using tophat2 (version 2.1.0) with option "--no-coverage search".
Gene expression (raw counts of mapped reads and FPKM) was obtained using Cufflinks (version 2.1.1)
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.
Submission date Nov 13, 2017
Last update date May 15, 2019
Contact name Takaho A. Endo
Organization name RIKEN
Department IMS
Lab Laboratory for Integrative Genomics
Street address 1-7-22 Suehiro, Tsurumi
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
Platform ID GPL18480
Series (2)
GSE106793 Temporal transcriptomic profiles of transition from hematopoietic multipotent progenitors to B committed cells [RNA-seq]
GSE106795 Temporal transcriptomic and epigenomic profiles of transition from hematopoietic multipotent progenitors to B committed cells
BioSample SAMN08014231
SRA SRX3384670

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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