|
| Status |
Public on Jun 08, 2023 |
| Title |
Erythroblasts_RNAseq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HD3
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: HD3
cell type: Chicken erythroblasts
genotype: WT
|
| Growth protocol |
Primary fibroblasts and HD3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO) supplemented with 10% fetal bovine serum (Biowest), 2% chicken serum and penicillin/streptomycin (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) following manufacturer's instructions. Libraries were prepared starting from 1 µg of RNA.
RNA-seq libraries were prepared A using the TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit (Illumina) following manufacturer's instructions.
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Erythroblast_1
|
| Data processing |
RNA-seq reads were mapped to the GRCg6a genome using STAR (v2.7.2b), raw counts were obtained using featureCounts and FPKM were calculated.
Because RNA content in chicken erythrocytes is significantly lower than in the other cell types, raw counts and FPKM were normalized for the number of cells required to obtain 1 µg of RNA
Assembly: GRCg6a
Supplementary files format and content: Tab-delimited text file including FPKM values for each sample.
|
| |
|
| Submission date |
Jun 15, 2022 |
| Last update date |
Jun 08, 2023 |
| Contact name |
Mayra Furlan-Magaril |
| E-mail(s) |
mfurlan@ifc.unam.mx
|
| Phone |
525512291890
|
| Organization name |
IFC-UNAM
|
| Department |
Molecular Genetics
|
| Lab |
Genome Topology
|
| Street address |
Circuito exterior s/n
|
| City |
Mexico City |
| State/province |
Mexico City |
| ZIP/Postal code |
04510 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL19005 |
| Series (2) |
| GSE206193 |
RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [RNA-seq] |
| GSE206194 |
RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes |
|
| Relations |
| BioSample |
SAMN29095140 |
| SRA |
SRX15713105 |
