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| Status |
Public on Jun 19, 2019 |
| Title |
XM001-iPSC_Rep4_Lane6 |
| Sample type |
SRA |
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| Source name |
Control iPS cells
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| Organism |
Homo sapiens |
| Characteristics |
genotype: WT
lane: Lane6
replicate: Replicate 4
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| Treatment protocol |
S1: definitive endoderm (3 d) Cells were first rinsed with 1× DPBS without Mg2+ and Ca2+ and then exposed to MCDB 131 medium (Life Technologies, Cat# 10372-019) further supplemented with 1.5 g/l sodium bicarbonate (Sigma, MO, Cat# S6297), 1× Glutamax (Life Technologies, Cat# 35050-079), 10 mM final glucose (Sigma, Cat# G8769) concentration, 0.5% bovine serum albumin fraction V, fatty acid free (Sigma, Cat# 10775835001), 100 ng/ml Activin-A (R&D Systems Inc, Cat# 338-AC-050/CF), and 3 μM or 5 μM of CHIR-99021 (GSK3β inhibitor, SelleckChem, Cat# S2924) for day 1. For day 2, cells were cultured in MCDB with 0.5% BSA, 1.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM glucose, 100 ng/ml Activin-A and 0.3 μM CHIR-99021. On day 3, cells were cultured in MCDB 131 with 0.5% BSA, 1.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM glucose and 100 ng/ml Activin-A. S2: primitive gut tube (2 d) Cells were rinsed with 1× DPBS without Mg2+ and Ca2+ and then exposed to MCDB 131 medium further supplemented with 1.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM final glucose concentration, 0.5% BSA, 0.25 mM ascorbic acid (Sigma, Cat# A4544), 50 ng/ml FGF7 (R & D Systems, Cat# 251-KG-010/CF) or/and 1.25 μM IWP-2 (Tocris Bioscience, Cat# 3533) for 2 d. S3: posterior foregut (2 d) Cells were then added for 2 d in MCDB 131 medium supplemented with 2.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM glucose concentration, 2% BSA, 0.25 mM ascorbic acid, 50 ng/ml FGF7, 0.25 μM SANT-1 (Sigma, Cat# S4572), 1 μM retinoic acid (RA; Sigma, Cat#R2625), 100 nM LDN193189 (LDN; BMP receptor inhibitor, Stemgent, CA, Cat#04-0019), 1:200 ITS-X (Life Technologies, Cat#51500056), and 200 nM TPB (PKC activator, custom synthesis, ChemPartner).
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| Growth protocol |
hiPSCs were cultured on 1:100 diluted Matrigel (BD Biosciences, CA, Cat #354277) in mTeSR™1 medium (STEMCELL technologies, Catalog # 85850). At ~70–80% confluency, cultures were rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen, Cat#14190) followed by incubation with TrypLE Select Enzyme (1x) (Life Technologies, Cat#12563011) for 3–5 min at 37 °C. Single cells were rinsed with mTeSR™1 medium, and spun at 1,000 rpm for 3 min. The resulting cell pellet was resuspended in mTeSR™1 medium supplemented with Y-27632 (10 μM; Sigma-Aldrich; MO, Cat#Y0503), and the single cell suspension was seeded at ~0.75 × 105 cells/cm2 on Matrigel-coated surfaces. Cultures were fed every day with mTeSR™1 medium and differentiation was initiated 72 h following seeding with ~90% starting confluency. All the cell lines were confirmed mycoplasma-free by using the Lonza MycoAlert Mycoplasma Detection Kit (Lonza, Cat# LT07-418).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from PDX1+/-, PDX1P33T/P33T, PDX1C18R/C18R and XM001 lines was extracted using miRNeasy Mini kit (Qiagen, #217004) and RNA integrity was checked using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Pico Kit).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina).
Stranded RNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
XM001-iPSC_Rep4_quant.sf
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| Data processing |
RNA-seq data was quantified from FASTQ files using salmon (0.11.3) quant with options --validateMappings --rangeFactorizationBins 4 --numBootstraps 100 --seqBias --gcBias.
Supplementary_files_format_and_content: SF file containg quantifications
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| Submission date |
Jan 28, 2019 |
| Last update date |
Jun 19, 2019 |
| Contact name |
Heiko Lickert |
| E-mail(s) |
heiko.lickert@helmholtz-munich.de
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| Organization name |
Helmholtz Zentrum München German Research Center for Environmental Health
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| Department |
Institute of Diabetes and Regeneration Research
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| Street address |
Ingolstaedter Landstraße 1
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| City |
Neuherberg |
| ZIP/Postal code |
85764 |
| Country |
Germany |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE125769 |
Point mutations in the PDX1 transactivation domain impair human β-cell development and function (RNA-Seq) |
| GSE125770 |
Point mutations in the PDX1 transactivation domain impair human β-cell development and function |
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| Relations |
| BioSample |
SAMN10833706 |
| SRA |
SRX5300563 |
| 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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