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| Status |
Public on Feb 14, 2022 |
| Title |
KDR+CXCR4+ replicate #2 |
| Sample type |
SRA |
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| Source name |
mesoderm
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| Organism |
Homo sapiens |
| Characteristics |
cell type: ES-derived mesoderm
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| Growth protocol |
The H1 hESC lines were maintained on irradiated mouse embryonic fibroblasts in hESC media. For differentiation, hPSC were cultured on matrigel-coated plasticware for 24 hours, followed by embryoid body generation. hPSCs were dissociated with brief trypsin-EDTA (0.05%) treatment, followed by scraping. Aggregates were resuspended in serum-free media (SFD) supplemented with L-glutamine (2 mM), ascorbic acid (1 mM), monothioglycerol (MTG, 4x10-4 M), transferrin (150 ug/mL), and BMP-4 (10 ng/mL). On day one, bFGF (5 ng/mL) was added. On day two, Activin A, SB-431542 (6 uM), CHIR99021 (3 uM), and/or IWP2 (3 uM) were added.
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| Extracted molecule |
total RNA |
| Extraction protocol |
KDR+CXCR4+ and KDR+CXCR4- cells were sorted using an BD Aria II. RNA was isolated with the miRNeasy Mini kit (Qiagen).
Libraries were prepared using the Clontech SMARTer kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
counts.txt
FPKM.txt
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| Data processing |
Basecalling with Illumina RTA 1.9.
Demultiplexing with custom demultipler written in python.
Fastq files were aligned to using STAR (version 2.7.1a).
Gene counts were obtained using Subread (version 1.6.5).
Expression values were filtered to only include protein coding genes using Ensembl BioMart.
FPKM calculation was performed using DESeq2 (version 1.24.0).
Genome_build: GENCODE GRCh38 version 23
Supplementary_files_format_and_content: Gene counts in tab-delimited text format.
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| Submission date |
Nov 01, 2019 |
| Last update date |
Feb 14, 2022 |
| Contact name |
Stephanie Luff |
| E-mail(s) |
stephanie.luff@mssm.edu
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Cell, Developmental, & Regenerative Biology
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| Lab |
Sturgeon
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| Street address |
1425 Madison Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE139838 |
Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells [CXCR4] |
| GSE139853 |
Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells |
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| Relations |
| BioSample |
SAMN13181007 |
| SRA |
SRX7087247 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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