|
Status |
Public on Apr 10, 2023 |
Title |
HUDEP1 RNA [100350] |
Sample type |
SRA |
|
|
Source name |
umbilical cord blood
|
Organism |
Homo sapiens |
Characteristics |
tissue: umbilical cord blood cell type: Human Umbilical Cord Blood-Derived Erythroid Progenitor cell line 1, abbreviated HUDEP1, expresses gamma-globin upon induced differentiation
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted from 1 million cells, using the RNeasy Mini Kit (Qiagen). The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used to enrich for polyA+ RNA and to create libraries for HiSeq2000 sequencing (Illumina).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/) Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR Gene quantification was done via RSEM Assembly: hg38 Supplementary files format and content: tab-separated values, TPM and counts
|
|
|
Submission date |
Apr 06, 2023 |
Last update date |
Jun 07, 2023 |
Contact name |
Ross Hardison |
E-mail(s) |
rch8@psu.edu
|
Organization name |
Pennsylvania State University
|
Street address |
303 Wartik Lab
|
City |
University Park |
State/province |
PA |
ZIP/Postal code |
16802 |
Country |
USA |
|
|
Platform ID |
GPL20301 |
Series (2) |
GSE229098 |
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes [human RNA] |
GSE229101 |
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes |
|
Relations |
BioSample |
SAMN34091148 |
SRA |
SRX19892453 |