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Sample GSM5993901

Query DataSets for GSM5993901

Status

Public on Aug 01, 2022

Title

Differentiation_CARMEN_C201-deleted_human_Adult_CPCs_Sample_3

Sample type

SRA

Source name

Human Fetal CPCs

Organism

Homo sapiens

Characteristics

cell type: Fetal CPCs

Growth protocol

Adult CPCs were expanded in expansion medium (3:1 DMEM 1g/l glucose/Medium 199 [Invitrogen] supplemented with 10% horse serum [Serotec, Kidlington, United Kingdom], 5% fetal bovine serum [Serotec], 100 U/ml penicillin [Invitrogen], and 100 μg/ml streptomycin [Invitrogen]). For inducing differentiation, cells were switched to MEM alpha (Invitrogen) containing 2% horse serum, 1 μmol/l dexamethasone (Sigma-Aldrich, St. Louis, Missouri), 50 μg/ml ascorbic acid (Sigma-Aldrich), 10 mmol/l β-glycerophosphate (Sigma-Aldrich), 100 U/ml penicillin (Invitrogen), and 100 μg/ml streptomycin (Invitrogen) (differentiation medium). Fetal CPCs were expanded in culture in proliferation medium, a 3:1 mixture of DMEM 1 g/L glucose and Medium 199 (Invitrogen) supplemented with 10% Horse serum (Serotec), 5% fetal bovine serum (Serotec), 100 U/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen). After three passages, cells were switched to a serum-free differentiation medium. Differentiation medium contained MEM alpha (Invitrogen) supplemented with 1 μM dexamethasone (Sigma-Aldrich), 50 μg/mL ascorbic acid (Sigma-Aldrich), 10 mM β-glycerophosphate (Sigma-Aldrich), 100 U/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen)

Extracted molecule

total RNA

Extraction protocol

Cells were lysed in Qiazol and RNA was purified using miRNeasy RNA prufication kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RIP-Seq

Library source

transcriptomic

Library selection

other

Instrument model

Illumina HiSeq 4000

Description

DKOC201S3

Data processing

Reads were pseudoaligned with kallisto software (version 0.44.0) to estimate the transcript level expression per sample
Gene level estimation was performed with sleuth R package (version 0.33.0) and transctipt expression was aggregated to gene level, followed by differential expression. For the transctipt to gene mapping gencode version 29 annotation was used.
Assembly: hg38
Supplementary files format and content: matrix table with TPM expression values for all genes and samples

Submission date

Apr 01, 2022

Last update date

Aug 01, 2022

Contact name

Mohamed Nemir

E-mail(s)

Mohamed.Nemir@chuv.ch

Organization name

Lausanne University Hospital

Department

Cœur et Vaisseau