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| Status |
Public on Feb 03, 2025 |
| Title |
Sample_I_transcriptome, KO |
| Sample type |
SRA |
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| Source name |
ESC
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H1_I_PFG, HUES8_I_PFG
cell type: ESC
editing strategy: enhancer, gene body
altered gene_symbol: PDX1, HES1, NEUROD1, PAX6, NKX2-2, ARX, GATA6, GATA4, FOXA2, FOXA1, RFX6, GLIS3, HHEX, UBA6, OTUD5, TADA2B, KDM2B, GSC, ONECUT1, MNX1, TET1, TET2, TET3, NANOG, BCOR, NEUROG3, BMPR1A, TLE3, NKX6-1, PBX1, QSER1, PROSER1, HNF4A
time (day): 7, 7
model system: posterior foregut (stage 3), posterior foregut (stage 3)
parental cell_line: H1, HUES8
pooled samples: 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Chromium Next GEM Single Cell 3สน GEM, Library & Gel Bead Kit v3.1
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Library name: Sample_I_transcriptome
I_star_unfiltered_counts.h5ad
I_star_unfiltered_features.h5ad
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| Data processing |
Unfiltered counts and feature counts (LARRY barcodes) generated for each library using STAR. Feature counts have been very slightly corrected for an edge case that affects about 1 in 10,000 counts. QC has been added and uploaded for the feature assignments. Feature assignment has also been done directly from the scRNA-seq expression as a control for the targeted sequence method (which is the main value in the features counts file). These are available in the 'expression' layer. Assignments have been provided for the features. These follow the original MSK criterion (minimum 10 counts - second best count no more than half of maximum). A second less restrictive assignment has also been provided using a minimum 4 counts - second best count no more than half of maximum). These are provided as obs 'feature-10' and 'feature-4'. These are provided as a convenience - filtering can still be done using whatever criteria the user wishes from the feature_counts file data.
https://github.com/morphic-bio/process_features
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: Unfiltered counts and feature counts per library as h5ad files. Zip folder includes QC files (.txt and .png) for expression feature assignments and targeted feature assignments.
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| Submission date |
Feb 03, 2025 |
| Last update date |
Feb 03, 2025 |
| Contact name |
MorPhiC Consortium |
| Organization name |
EMBL-EBI
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| Street address |
Wellcome Genome Campus
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| City |
Hinxton |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE288587 |
Mapping the Temporal Impact of Perturbations on Lineage Plasticity and Gene Regulation |
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| Relations |
| BioSample |
SAMEA117610454 |
| SRA |
ERX13563861 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8770310_I_star_unfiltered_counts.h5ad |
4.4 Gb |
(ftp)(http) |
H5AD |
| GSM8770310_I_star_unfiltered_features.h5ad |
321.9 Mb |
(ftp)(http) |
H5AD |
SRA Run Selector |
| Raw data are available in SRA |
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