ALLEN CELL EXPLORER
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      4. └ Z-stack viewer
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      3. └ Z-stack viewer
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Genomics

Explore and download genomics and transcriptomics data

Overview

The Allen Institute for Cell Science has generated a collection of fluorescently tagged hiPSC clonal lines representing the major structures of the cell. All cell lines were generated using the wild type C hiPS cell line (WTC line) as the parental cell line. To establish a reference profile, we performed whole genome sequencing and population RNA-Seq on the WTC line. As part of our quality control process, we use whole exome sequencing and population RNA-Seq to evaluate any changes in the transcriptional profiles and exomes of our fluorescently tagged hiPSC lines relative to the parental WTC line. Raw data is available upon request - please email ​[email protected].
Picture

Parental WTC Genome

Explore the parental WTC short read whole genome sequence and variants in the UCSC Genome Browser: 
WTC whole genome track
Download the parental WTC whole genome raw data and variant calls: 
WTC short read whole genome
WTC linked read whole genome

Tagged Line Exomes

Explore the exomes and variants for our fluorescently tagged lines in the UCSC Genome Browser or download raw data and variant calls. One clone (public clone) for each gene tag is publicly available through Coriell.
Exome raw data
Cell line & UCSC link
Gene
Tag
Public clone
AICS-5
PXN
EGFP
50
AICS-10
SEC61B
mEGFP
55
AICS-11
TOMM20
mEGFP
27
AICS-12
TUBA1B
mEGFP
105
AICS-13
LMNB1
mEGFP
210
AICS-14
FBL
mEGFP
6
AICS-16
ACTB
mEGFP
184
AICS-17
DSP
​mEGFP
65
AICS-22
LAMP1
mEGFP
37
AICS-23
TJP1
mEGFP
84
AICS-24
MYH10
mEGFP
80
AICS-25
ST6GAL1
mEGFP
1 (mono-allelic); 44 (bi-allelic)
AICS-30
MAP1LC3B
mEGFP
22
AICS-31
TUBA1B
mTag-RFP-T
35
AICS-32
CETN2
mTag-RFP-T
19
AICS-33
SLC25A17
mEGFP
115
AICS-37
TNNI1
mEGFP
172
AICS-40
RAB5A
mEGFP
13 (mono-allelic); 35 (bi-allelic)
AICS-46
ATP2A2
mEGFP
51
AICS-53
GJA1
mEGFP
16
AICS-54
AAVS1
mTagRFPT-CAAX
91
AICS-57
NPM1
mEGFP
50
AICS-58
CTNNB1
mEGFP
67
AICS-61
HIST1H2BJ
mEGFP
36
AICS-69
NUP153
mEGFP
88

Transcriptional Profiles

​Download the transcriptional profiles of the parental WTC line and 13 fluorescently tagged lines. 
Transcriptomics v1.2 .zip
Download our single cell RNA-sequencing data set of hiPSCs undergoing cardiac differentiation on Quilt. Data set includes 4 time points, 3 cell lines, 2 differentiation protocols, and multiple experimental replicates
scRNA-seq dataset on Quilt
Transcriptomics v1.2.zip

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Allen Institute for Cell Science is a part of the Allen Institute. The mission of the Allen Institute is to understand the principles that govern life, and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.
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  • About
      Institute
      1. Our science: CellScapes
      2. Past foundational projects
      3. News feed
      4. About us
      5. Careers
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Disease Collection Cell Catalog
      3. Cell Catalog quickview
      4. Cell video shorts
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
      4. Support forum
      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data: Images, genomics, & features
  • Data & Digital Tools
      General
      1. Tools and resources overview
      2. Download cell data (images, genomics, features)
      3. Code repositories & software
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Web tools
      1. BioFile Finder
      2. Cell Feature Explorer
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      Web tools (con't)
      1. Simularium viewer
      2. Timelapse Feature Explorer
      3. Visual Guide to Human Cells
      4. Vol-E (Web Volume Viewer)
      5. 3D Cell Viewer
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Allen Integrated Cell
      6. └ 3D Probabilistic Modeling
      7. └ Label-free Determination
      4D biology models
      1. Simularium viewer
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. Publications
      2. Preprints
      Presentations
      1. Talks & posters
  • Education
      Educational resources
      1. All resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. 3D Cell Feature Explorer
      4. 3D Cell Viewer
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Video tutorials
      2. Visual Guide tutorial
      3. AGAVE documentation
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
  • 🔍
      SEARCHBAR