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Sample GSM5373540 Query DataSets for GSM5373540
Status Public on Jan 27, 2022
Title d0d4_earlydiff
Sample type SRA
Source name differentiating embryonic stem cells
Organism Mus musculus
Characteristics time: day 0 through day 4
developmental stage: embryonic stem cells undergoing differentiation to early gastrulation
Treatment protocol mESCs were removed from feeder cells and cultured in suspension in serum-free differentiation media (SFD) from day0 to day 2. At day 2, four different primitive streak induction treatments were established by adding growth factors Wnt3a (25 ng/mL) and Activin A (9 ng/mL) alone or with one of the following additional growth factors: Noggin (150 ng/mL) Gsk3 inhibitor (10 mM), or Bmp4 (0.5 ng/mL).
Growth protocol GFP-Bracyury mESC cells were maintained on mouse embryonic feeder (mEF) cells in Dulbecco's Modified Eagles' Medium (DMEM; Gibco) containing 15% FBS (Sigmal-Aldrich), 1% PSG (Gibco), LIF (MTI Global Stem; 1,000 U/mL), and 2-mercaptoethanol (Sigma; 0.1mM).
Extracted molecule polyA RNA
Extraction protocol Single-cell samples were prepared by dissocaiting cells in TrypLE before strained through a 40 uM cell strainer.
Sample barcoding and library preparation was carried out using the MULTI-seq protocol (McGinnis et al. 2019).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Sequencing alignment to the mm10 reference genome was performed using CellRanger (version 3.1), and spliced, unspliced, and ambiguous read counts were extracted using Velocyto.
Sample barcode classification was performed using the deMULTIplex R package, and doublets and negatives were removed.
Normalization, log transformation, and other data processing carried out in Scanpy (version 1.4.5; Wolf et al., 2018).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data, including cluster assignments, provided in h5ad format. Cell metadata (names, timepoint, treatment, cluster, etc.) are stored in .obs. Raw counts data is stored in .raw. Normalized and log-transformed data is stored in .X.
Submission date Jun 11, 2021
Last update date Jan 27, 2022
Contact name Patrick Cahan
Organization name Johns Hopkins University School of Medicine
Department ICE and Biomedical Engineering
Lab Cahan Lab
Street address 733 North Broadway, MRB 653
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platform ID GPL24247
Series (1)
GSE177051 Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification
BioSample SAMN19671526
SRA SRX11122147

Supplementary file Size Download File type/resource
GSM5373540_early_diff.h5ad.gz 88.0 Mb (ftp)(http) H5AD
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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