|
| Status |
Public on Mar 06, 2018 |
| Title |
FL iLS_24h after treatment rep3 |
| Sample type |
SRA |
| |
|
| Source name |
FL iLS_24h after treatment
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: fetal liver induced leukocyte stem cell (FL iLS)
time point: 24h 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 |
S02475
|
| 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 |
| E-mail(s) |
takaho.endo@riken.jp
|
| 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 |
|
| Relations |
| BioSample |
SAMN08014215 |
| SRA |
SRX3384679 |
