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Sample GSM5554216 Query DataSets for GSM5554216
Status Public on Sep 30, 2021
Title Ex_vivo_erythroid_Donor3_Day1 RNA-seq
Sample type SRA
 
Source name CD34_RO03280
Organism Homo sapiens
Characteristics cell type: CD34+
differentiation day: 1
Growth protocol We used a 2-step differentiation protocol as described in Giarratana et al., 2011, Blood. Briefly, frozen CD34+ HSPCs are conditioned overnight in serum-free media in the presence of FLT3, TPO and IL3. Cells were then transferred in Step 1, serum-free media supplemented with BSA, Insulin, human-holotransferrin, heparin, hydrocortisone, human recombinant IL-3, hrEPO, and hrSCF and maintained for 7 days. On day 8, cells were transferred to Step 2 media where we withdraw hydrocortisone and IL-3 and maintain the rest of the components. Cells are maintained in Step 2 media until culture termination on day 12.
Extracted molecule total RNA
Extraction protocol Approximately 200,000 cells were collected per culture and total RNA was isolated using QIAGEN RNeasy kit per manufacturer's instructions
RNA library was constructed using the Illumina RNA TruSeq Stranded tRNA with Ribo-Zero Globin
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Basecalling, RTA v3.4.4
Alignments to GRCh38, star v2.4.2a
Annotation, cufflinks v2.2.1, GENCODE v25
Subread, featureCounts v1.5.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Cufflinks FPKM expression levels per gene as a .txt file
 
Submission date Sep 02, 2021
Last update date Sep 30, 2021
Contact name Grigorios Georgolopoulos
E-mail(s) ggeorgol@altius.org
Organization name Altius Institute
Street address 2211 Elliott Ave #400
City Seattle
State/province WA
ZIP/Postal code 98121
Country USA
 
Platform ID GPL20301
Series (2)
GSE182816 Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation
GSE183266 Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation [RNA-seq]
Relations
BioSample SAMN21206500
SRA SRX11996011

Supplementary file Size Download File type/resource
GSM5554216_AG7356.genes.fpkm_tracking.gz 1.5 Mb (ftp)(http) FPKM_TRACKING
GSM5554216_AG7356.isoforms.fpkm_tracking.gz 2.9 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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