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| Status |
Public on Sep 22, 2021 |
| Title |
CTRL_LINE2_iPSC_ARID1B |
| Sample type |
SRA |
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| Source name |
Control_Line_2 (GM23716 line)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Induced_Pluripotent_Stem_Cells
antibodies: ARID1B Abcam ab57461
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| Treatment protocol |
Stem cells were differentiated in CNCC using a previously published protocol (Prescot et al.2015). iPSCs were treated with CNCC Derivation media: 1:1 Neurobasal medium/D-MEM F-12 medium,B-27 supplement, N-2 supplement, 20 ng/ml bFGF, 20 ng/ml EGF, 5 µg/ml bovine insulin and 1× Glutamax-I supplement. Three days after the appearance of the migratory CNCC, cells were detached using accutase and placed into geltrex-coated plates. The early migratory CNCCs were then transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, B-27 supplement, N2 supplement , 20 ng/ml , 20 ng/ml EGF, 1 mg/ml bovine serum albumin and 1× Glutamax-I supplement
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| Growth protocol |
The iPSC lines were expanded in feeder-free, serum-free mTeSR™1 medium (STEMCELL Technologies). Cells were passaged ~1:10 at 80% confluency using ReLeSR (STEMCELL Technologies) and small cell clusters (50–200 cells) were subsequently plated on tissue culture dishes coated overnight with Geltrex™ LDEV-Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix (Fisher-Scientific).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA-seq Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library
ATAC-seq: 50000 cells per condition were processed as described in the original ATAC-seq protocol paper (Buenrostro et al 2013)
ChIP-seq: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NextSeq 500, producing 75bp SE reads.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
ChIP-seq and ATAC-seq data were aligned to hg19 using BWA-mem
ATAC-seq and CHIP-seq peaks were called with MACS2
For input bigwig was made with Deeptools
Genome_build: Hg19
Supplementary_files_format_and_content: peak text files (ChIP-seq, ATAC-seq), Bigwig for input of Chip-seq
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| Submission date |
Aug 21, 2021 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Marco Trizzino |
| E-mail(s) |
[email protected]
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| Phone |
07521215018
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| Organization name |
Imperial College London
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| Department |
Life Sciences
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| Street address |
Imperial College Road
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| City |
London |
| State/province |
UK |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE169654 |
Impaired attenuation of pluripotency enhancers at the onset of neural crest formation in ARID1B haploinsufficient Coffin-Siris patients |
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| Relations |
| BioSample |
SAMN20923904 |
| SRA |
SRX11857212 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5530975_CTRL_LINE2_iPSC_ARID1B_normalized.bw |
266.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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