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Sample GSM5554283 Query DataSets for GSM5554283
Status Public on Sep 30, 2021
Title Ex_vivo_Ery_day_6 scRNA-seq
Sample type SRA
 
Source name CD34_RO03183
Organism Homo sapiens
Characteristics cell type: CD34+
differentiation day: 6
Growth protocol We used a 2-step erythroid 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. CD34+ HSPCs were differentiated to the megakaryocyte lineage by culturing for 11 days in IMDM based media containing 30ng/mL rhTPO , 1ng/mL rhSCF , 7.5ng/mL rhIL-6 , 13.5ng/mL rhIL-9 , 20% BIT , 40µg/mL LDL , 0.05mM beta mercaptoethanol
Extracted molecule total RNA
Extraction protocol Frozen culture cell suspension from ex vivo erythroid or megakaryocytic culture or uncultured CD34+ were thawed and resuspended in PBS-BSA aiming for ~5,000 cell per sample
Single cells were lysed in droplets using the 10X Chromium instrument Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev A
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description 10X Single Cell 3' Reagent Kit V1
Data processing Library strategy: scRNA-seq
FASTQ files were demultiplexed using cellranger demux with default parameters
BAM files were generated using 10X Genomics Cellranger V1.3 using default parameters
Gene-barcode (count) matrices were generated using 10X Genomics Cellranger V1.3 using default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell barcodes in tab separated file
Supplementary_files_format_and_content: Gene list in tab separated file
Supplementary_files_format_and_content: Cell-gene count matrix .mtx formatted
 
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
GSE183267 Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation [scRNA-seq]
Relations
BioSample SAMN21206784
SRA SRX11996082

Supplementary file Size Download File type/resource
GSM5554283_Ex_vivo_Ery_day_6.barcodes.tsv.gz 12.5 Kb (ftp)(http) TSV
GSM5554283_Ex_vivo_Ery_day_6.genes.tsv.gz 484.6 Kb (ftp)(http) TSV
GSM5554283_Ex_vivo_Ery_day_6.matrix.mtx.gz 19.5 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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