|
| Status |
Public on Mar 29, 2017 |
| Title |
Bloodlinc_sh1 |
| Sample type |
SRA |
| |
|
| Source name |
fetal liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: fetal liver
developmental stage: E14.5
|
| Growth protocol |
Erythroid progenitors were purified from E14.5 mouse fetal livers by magnetic-assisted cell sorting (Flygare et al., 2011) and cultured for 24hrs in erythropoietin-containing media to induce terminal proliferation and differentiation (Zhang et al., 2003).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, total RNA was isolated using the miRNeasy kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was depleted from 4ug total RNA using the Ribo-Zero Gold Kit (Epicentre, Madison, WI).
Strand-specific cDNA libraries were prepared using a dUTP marking protocol (Borodina et al., 2011) and sequenced on an Illumina HiSeq2000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
total RNA minus rRNA
|
| Data processing |
Reads were mapped to mm9 using TopHat v2.0.11 (Trapnell et al. 2009) with “--min-anchor 5 --no-novel-juncs” parameters. Gene expression was quantified from the mapped reads using HTSeq (Anders et al. 2015) on “union” mode based on Ensembl version 67 gene annotations
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files containing Htseq output for each sample
|
| |
|
| Submission date |
Mar 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan R Alvarez-Dominguez |
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE97120 |
The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans (RNA-seq) |
| GSE97121 |
The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans |
|
| Relations |
| BioSample |
SAMN06647519 |
| SRA |
SRX2676970 |
