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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

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

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cellscience.alleninstitute.org
  • About
    • What We Do
    • FAQs
    • Videos & Tutorials
    • Site Updates
    • < Forum >
    • < AllenInstitute.org >
  • Animated Cell
    • Educational Resources
    • Visual Guide to Human Cells
    • Visual Guide Tutorial
    • Research Projects >
      • Pathtrace rendering
  • Cells & Biology
    • Cell Catalog
    • About our Cells >
      • hiPS Cell Biology Overview
      • Cell Structure Observations
      • Cell Catalog QuickView
    • Genomics
    • Methods & SOPs >
      • Methods for Cells in the Lab
      • Cell Methods: Videos from the Lab
      • Methods for Microscopy
    • Research Projects >
      • hiPS Cells During Mitosis
      • Drug Perturbation Pilot
      • Differentiation Into Cardiomyocytes
      • Why Endogenous Tagging?
  • Data & Tools
    • Cell Catalog
    • 3D Cell Viewer
    • Cell Feature Explorer
    • Integrated Mitotic Stem Cell Z-stack Viewer
    • Deep Cell Zoom
    • Segmenter
    • Data Downloading
    • Software & Code
    • Simularium
    • Research Projects >
      • Extracting Information
  • Modeling & Analysis
    • Integrated Mitotic Stem Cell
    • Allen Integrated Cell
    • Label-free Determination
    • Data Notebook Exploration >
      • Cell Shape Analysis
      • Programmatic Data Access
    • Research Projects >
      • 3D Probabilistic Modeling
  • News & Publications
    • News Feed
    • Publications
    • Archived Content