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Genomics

Explore & download genomics & 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 ​cells@alleninstitute.org.
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

Transcriptomics v1.2 .zip
​Download the transcriptional profiles of the parental WTC line and 13 fluorescently tagged lines. 

scRNA-seq dataset on Quilt
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
Transcriptomics v1.2.zip

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  • About
      Institute
      1. News feed
      2. What we do
      3. Publications
      4. Allen Institute | allenInstitute.org
      5. Careers
      Site
      1. Home page
      2. Site updates
      3. Archived content
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      4. Support forum
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
      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
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. All journal publications
      2. Preprints (biorxiv, arxiv)
      Posters
      1. Select posters
  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Digital tool tutorials with videos
      2. Visual Guide tutorial
      3. AGAVE user guide
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
  • 🔍
      SEARCHBAR