|
| Status |
Public on Jan 01, 2023 |
| Title |
G1ER_WT_bE_0h |
| Sample type |
SRA |
| |
|
| Source name |
G1ER cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: G1ER
cell type: erythroblasts
genotype: wild-type
treatment: estradiol
|
| Treatment protocol |
G1ER cells were differentiated with beta-estradiol for 24 hours.
|
| Growth protocol |
Wild type and CHD7 knockout G1ER cells were grown and maintained in IMDM media containing heat-inactivated FBS (16%), pen/strep (2%), monothioglycerol (6.2 mL per 500 mL), EPO (2U/mL) and SCF conditioned media (0.6%). Cells were differentiated with beta-estradiol (10-7M final concentration). After 24 hrs of beta-estradiol treatment, differentiation was assessed using benzidine staining method (using o-diansidine from Sigma, D9143, ref – Orkin SH, Harosi FI, Leder P. PNAS 72 (1): 98-102, 1975).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from one million cells was isolated with Trizol according to the manufacturer’s instructions. The RNA was DNAse treated using the RNase free DNase set from Qiagen (79254) according to the instructions. The whole amount of RNA was treated with the Ribo-Zero Gold kit (Human/Mouse/Rat, Epicentre) according to the manufacturer’s instructions.
Ribo-zero treated RNA was used to create multiplexed RNA-seq libraries using the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ribosomal depleted RNA
AC1-G1ER-bE
|
| Data processing |
Quality control of RNA-Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions.
High-quality reads were aligned to UCSC build GRCm38 of the mouse genome using Tophat 2.0.11 without novel splicing form calls.
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1.
FPKM values were used to normalize and quantify each transcript.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Excel summary file of transcript abundance.
|
| |
|
| Submission date |
Jul 07, 2016 |
| Last update date |
Jan 01, 2023 |
| Contact name |
Leonard Zon |
| E-mail(s) |
zon@enders.tch.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
Oncology/Hematology
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE84128 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [RNA-seq] |
| GSE84131 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation |
|
| Relations |
| BioSample |
SAMN05363836 |
| SRA |
SRX1901640 |
